[Galaxy S 4 i9505 Original Android Development] broodplank1337:
Hmm thats kinda odd, ill check if I can fix it

try this updater-script:

show_progress(0.500000, 0);
mount("ext4", "EMMC", "/dev/block/platform/msm_sdcc.1/by-name/system", "/system");
package_extract_dir("system", "/system");
symlink("Roboto-Bold.ttf", "/system/fonts/DroidSans-Bold.ttf");
symlink("Roboto-Regular.ttf", "/system/fonts/DroidSans.ttf");
symlink("busybox", "/system/xbin/[", "/system/xbin/[[",
"/system/xbin/adjtimex", "/system/xbin/arp", "/system/xbin/ash",
"/system/xbin/awk", "/system/xbin/base64", "/system/xbin/basename",
"/system/xbin/bbconfig", "/system/xbin/blkid", "/system/xbin/blockdev",
"/system/xbin/brctl", "/system/xbin/bunzip2", "/system/xbin/bzcat",
"/system/xbin/bzip2", "/system/xbin/cal", "/system/xbin/cat",
"/system/xbin/catv", "/system/xbin/chattr", "/system/xbin/chgrp",
"/system/xbin/chmod", "/system/xbin/chown", "/system/xbin/chroot",
"/system/xbin/clear", "/system/xbin/cmp", "/system/xbin/comm",
"/system/xbin/cp", "/system/xbin/cpio", "/system/xbin/crond",
"/system/xbin/crontab", "/system/xbin/cut", "/system/xbin/date",
"/system/xbin/dc", "/system/xbin/dd", "/system/xbin/depmod",
"/system/xbin/devmem", "/system/xbin/df", "/system/xbin/diff",
"/system/xbin/dirname", "/system/xbin/dmesg", "/system/xbin/dnsd",
"/system/xbin/dos2unix", "/system/xbin/du", "/system/xbin/echo",
"/system/xbin/ed", "/system/xbin/egrep", "/system/xbin/env",
"/system/xbin/expand", "/system/xbin/expr", "/system/xbin/false",
"/system/xbin/fbsplash", "/system/xbin/fdisk", "/system/xbin/fgrep",
"/system/xbin/find", "/system/xbin/flash_lock",
"/system/xbin/flash_unlock", "/system/xbin/flashcp",
"/system/xbin/flock", "/system/xbin/fold", "/system/xbin/free",
"/system/xbin/freeramdisk", "/system/xbin/fstrim", "/system/xbin/fsync",
"/system/xbin/ftpget", "/system/xbin/ftpput", "/system/xbin/fuser",
"/system/xbin/getopt", "/system/xbin/grep", "/system/xbin/groups",
"/system/xbin/gunzip", "/system/xbin/gzip", "/system/xbin/halt",
"/system/xbin/head", "/system/xbin/hexdump", "/system/xbin/id",
"/system/xbin/ifconfig", "/system/xbin/inetd", "/system/xbin/insmod",
"/system/xbin/install", "/system/xbin/ionice", "/system/xbin/iostat",
"/system/xbin/ip", "/system/xbin/kill", "/system/xbin/killall",
"/system/xbin/killall5", "/system/xbin/less", "/system/xbin/ln",
"/system/xbin/losetup", "/system/xbin/ls", "/system/xbin/lsattr",
"/system/xbin/lsmod", "/system/xbin/lsusb", "/system/xbin/lzcat",
"/system/xbin/lzma", "/system/xbin/lzop", "/system/xbin/lzopcat",
"/system/xbin/man", "/system/xbin/md5sum", "/system/xbin/mesg",
"/system/xbin/mkdir", "/system/xbin/mke2fs", "/system/xbin/mkfifo",
"/system/xbin/mkfs.ext2", "/system/xbin/mkfs.vfat",
"/system/xbin/mknod", "/system/xbin/mkswap", "/system/xbin/mktemp",
"/system/xbin/modinfo", "/system/xbin/modprobe", "/system/xbin/more",
"/system/xbin/mount", "/system/xbin/mountpoint", "/system/xbin/mpstat",
"/system/xbin/mv", "/system/xbin/nanddump", "/system/xbin/nandwrite",
"/system/xbin/nbd-client", "/system/xbin/netstat", "/system/xbin/nice",
"/system/xbin/nohup", "/system/xbin/nslookup", "/system/xbin/ntpd",
"/system/xbin/od", "/system/xbin/patch", "/system/xbin/pgrep",
"/system/xbin/pidof", "/system/xbin/ping", "/system/xbin/pipe_progress",
"/system/xbin/pkill", "/system/xbin/pmap", "/system/xbin/poweroff",
"/system/xbin/printenv", "/system/xbin/printf", "/system/xbin/ps",
"/system/xbin/pstree", "/system/xbin/pwd", "/system/xbin/pwdx",
"/system/xbin/rdev", "/system/xbin/readlink", "/system/xbin/realpath",
"/system/xbin/renice", "/system/xbin/reset", "/system/xbin/resize",
"/system/xbin/rev", "/system/xbin/rm", "/system/xbin/rmdir",
"/system/xbin/rmmod", "/system/xbin/route", "/system/xbin/run-parts",
"/system/xbin/rx", "/system/xbin/sed", "/system/xbin/seq",
"/system/xbin/setconsole", "/system/xbin/setserial",
"/system/xbin/setsid", "/system/xbin/sh", "/system/xbin/sha1sum",
"/system/xbin/sha256sum", "/system/xbin/sha3sum",
"/system/xbin/sha512sum", "/system/xbin/sleep", "/system/xbin/sort",
"/system/xbin/split", "/system/xbin/stat", "/system/xbin/strings",
"/system/xbin/stty", "/system/xbin/sum", "/system/xbin/swapoff",
"/system/xbin/swapon", "/system/xbin/sync", "/system/xbin/sysctl",
"/system/xbin/tac", "/system/xbin/tail", "/system/xbin/tar",
"/system/xbin/taskset", "/system/xbin/tee", "/system/xbin/telnet",
"/system/xbin/telnetd", "/system/xbin/test", "/system/xbin/tftp",
"/system/xbin/tftpd", "/system/xbin/time", "/system/xbin/timeout",
"/system/xbin/top", "/system/xbin/touch", "/system/xbin/tr",
"/system/xbin/traceroute", "/system/xbin/true", "/system/xbin/ttysize",
"/system/xbin/tune2fs", "/system/xbin/umount", "/system/xbin/uname",
"/system/xbin/uncompress", "/system/xbin/unexpand", "/system/xbin/uniq",
"/system/xbin/unix2dos", "/system/xbin/unlzma", "/system/xbin/unlzop",
"/system/xbin/unxz", "/system/xbin/unzip", "/system/xbin/uptime",
"/system/xbin/usleep", "/system/xbin/uudecode", "/system/xbin/uuencode",
"/system/xbin/vi", "/system/xbin/watch", "/system/xbin/wc",
"/system/xbin/wget", "/system/xbin/which", "/system/xbin/whoami",
"/system/xbin/xargs", "/system/xbin/xz", "/system/xbin/xzcat",
"/system/xbin/yes",
"/system/xbin/zcat");
symlink("libGLESv2.so", "/system/lib/libGLESv3.so");
symlink("logcat", "/system/bin/lolcat");
symlink("mksh", "/system/bin/sh");
symlink("mount.exfat", "/system/bin/fsck.exfat",
"/system/bin/mkfs.exfat");
symlink("toolbox", "/system/bin/cat", "/system/bin/chcon",
"/system/bin/chmod", "/system/bin/chown", "/system/bin/clear",
"/system/bin/cmp", "/system/bin/cp", "/system/bin/date",
"/system/bin/dd", "/system/bin/df", "/system/bin/dmesg",
"/system/bin/du", "/system/bin/getenforce", "/system/bin/getevent",
"/system/bin/getprop", "/system/bin/getsebool", "/system/bin/grep",
"/system/bin/hd", "/system/bin/id", "/system/bin/ifconfig",
"/system/bin/iftop", "/system/bin/insmod", "/system/bin/ioctl",
"/system/bin/ionice", "/system/bin/kill", "/system/bin/ln",
"/system/bin/load_policy", "/system/bin/log", "/system/bin/ls",
"/system/bin/lsmod", "/system/bin/lsof", "/system/bin/md5",
"/system/bin/mkdir", "/system/bin/mkswap", "/system/bin/mount",
"/system/bin/mv", "/system/bin/nandread", "/system/bin/netstat",
"/system/bin/newfs_msdos", "/system/bin/notify", "/system/bin/printenv",
"/system/bin/ps", "/system/bin/r", "/system/bin/readlink",
"/system/bin/renice", "/system/bin/restart", "/system/bin/restorecon",
"/system/bin/rm", "/system/bin/rmdir", "/system/bin/rmmod",
"/system/bin/route", "/system/bin/runcon", "/system/bin/schedtop",
"/system/bin/sendevent", "/system/bin/setconsole",
"/system/bin/setenforce", "/system/bin/setfattr", "/system/bin/setprop",
"/system/bin/setsebool", "/system/bin/sleep", "/system/bin/smd",
"/system/bin/start", "/system/bin/stop", "/system/bin/swapoff",
"/system/bin/swapon", "/system/bin/sync", "/system/bin/top",
"/system/bin/touch", "/system/bin/umount", "/system/bin/uptime",
"/system/bin/vmstat", "/system/bin/watchprops",
"/system/bin/wipe");
set_metadata_recursive("/system", "uid", 0, "gid", 0, "dmode", 0755, "fmode", 0644, "capabilities", 0x0, "selabel", "u:object_r:system_file:s0");
set_metadata_recursive("/system/bin", "uid", 0, "gid", 2000, "dmode", 0755, "fmode", 0755, "capabilities", 0x0, "selabel", "u:object_r:system_file:s0");
set_metadata("/system/bin/app_process", "uid", 0, "gid", 2000, "mode", 0755, "capabilities", 0x0, "selabel", "u:object_r:zygote_exec:s0");
set_metadata("/system/bin/clatd", "uid", 0, "gid", 2000, "mode", 0755, "capabilities", 0x0, "selabel", "u:object_r:clatd_exec:s0");
set_metadata("/system/bin/debuggerd", "uid", 0, "gid", 2000, "mode", 0755, "capabilities", 0x0, "selabel", "u:object_r:debuggerd_exec:s0");
set_metadata("/system/bin/dhcpcd", "uid", 0, "gid", 2000, "mode", 0755, "capabilities", 0x0, "selabel", "u:object_r:dhcp_exec:s0");
set_metadata("/system/bin/dnsmasq", "uid", 0, "gid", 2000, "mode", 0755, "capabilities", 0x0, "selabel", "u:object_r:dnsmasq_exec:s0");
set_metadata("/system/bin/drmserver", "uid", 0, "gid", 2000, "mode", 0755, "capabilities", 0x0, "selabel", "u:object_r:drmserver_exec:s0");
set_metadata("/system/bin/efsks", "uid", 0, "gid", 2000, "mode", 0755, "capabilities", 0x0, "selabel", "u:object_r:kickstart_exec:s0");
set_metadata("/system/bin/hostapd", "uid", 0, "gid", 2000, "mode", 0755, "capabilities", 0x0, "selabel", "u:object_r:hostapd_exec:s0");
set_metadata("/system/bin/installd", "uid", 0, "gid", 2000, "mode", 0755, "capabilities", 0x0, "selabel", "u:object_r:installd_exec:s0");
set_metadata("/system/bin/keystore", "uid", 0, "gid", 2000, "mode", 0755, "capabilities", 0x0, "selabel", "u:object_r:keystore_exec:s0");
set_metadata("/system/bin/ks", "uid", 0, "gid", 2000, "mode", 0755, "capabilities", 0x0, "selabel", "u:object_r:kickstart_exec:s0");
set_metadata("/system/bin/mediaserver", "uid", 0, "gid", 2000, "mode", 0755, "capabilities", 0x0, "selabel", "u:object_r:mediaserver_exec:s0");
set_metadata("/system/bin/mksh", "uid", 0, "gid", 2000, "mode", 0755, "capabilities", 0x0, "selabel", "u:object_r:shell_exec:s0");
set_metadata("/system/bin/mtpd", "uid", 0, "gid", 2000, "mode", 0755, "capabilities", 0x0, "selabel", "u:object_r:mtp_exec:s0");
set_metadata("/system/bin/netcfg", "uid", 0, "gid", 3003, "mode", 02750, "capabilities", 0x0, "selabel", "u:object_r:system_file:s0");
set_metadata("/system/bin/netd", "uid", 0, "gid", 2000, "mode", 0755, "capabilities", 0x0, "selabel", "u:object_r:netd_exec:s0");
set_metadata("/system/bin/ping", "uid", 0, "gid", 0, "mode", 0755, "capabilities", 0x0, "selabel", "u:object_r:ping_exec:s0");
set_metadata("/system/bin/pppd", "uid", 0, "gid", 2000, "mode", 0755, "capabilities", 0x0, "selabel", "u:object_r:ppp_exec:s0");
set_metadata("/system/bin/qcks", "uid", 0, "gid", 2000, "mode", 0755, "capabilities", 0x0, "selabel", "u:object_r:kickstart_exec:s0");
set_metadata("/system/bin/racoon", "uid", 0, "gid", 2000, "mode", 0755, "capabilities", 0x0, "selabel", "u:object_r:racoon_exec:s0");
set_metadata("/system/bin/rild", "uid", 0, "gid", 2000, "mode", 0755, "capabilities", 0x0, "selabel", "u:object_r:rild_exec:s0");
set_metadata("/system/bin/run-as", "uid", 0, "gid", 2000, "mode", 0750, "capabilities", 0xc0, "selabel", "u:object_r:runas_exec:s0");
set_metadata("/system/bin/sdcard", "uid", 0, "gid", 2000, "mode", 0755, "capabilities", 0x0, "selabel", "u:object_r:sdcardd_exec:s0");
set_metadata("/system/bin/servicemanager", "uid", 0, "gid", 2000, "mode", 0755, "capabilities", 0x0, "selabel", "u:object_r:servicemanager_exec:s0");
set_metadata("/system/bin/surfaceflinger", "uid", 0, "gid", 2000, "mode", 0755, "capabilities", 0x0, "selabel", "u:object_r:surfaceflinger_exec:s0");
set_metadata("/system/bin/vold", "uid", 0, "gid", 2000, "mode", 0755, "capabilities", 0x0, "selabel", "u:object_r:vold_exec:s0");
set_metadata("/system/bin/wpa_supplicant", "uid", 0, "gid", 2000, "mode", 0755, "capabilities", 0x0, "selabel", "u:object_r:wpa_exec:s0");
set_metadata_recursive("/system/etc/dhcpcd", "uid", 0, "gid", 0, "dmode", 0755, "fmode", 0644, "capabilities", 0x0, "selabel", "u:object_r:dhcp_system_file:s0");
set_metadata("/system/etc/dhcpcd/dhcpcd-run-hooks", "uid", 1014, "gid", 2000, "mode", 0550, "capabilities", 0x0, "selabel", "u:object_r:dhcp_system_file:s0");
set_metadata_recursive("/system/etc/ppp", "uid", 0, "gid", 0, "dmode", 0755, "fmode", 0555, "capabilities", 0x0, "selabel", "u:object_r:ppp_system_file:s0");
set_metadata("/system/vendor", "uid", 0, "gid", 2000, "mode", 0755, "capabilities", 0x0, "selabel", "u:object_r:system_file:s0");
set_metadata("/system/vendor/firmware", "uid", 0, "gid", 2000, "mode", 0755, "capabilities", 0x0, "selabel", "u:object_r:system_file:s0");
set_metadata("/system/vendor/lib", "uid", 0, "gid", 2000, "mode", 0755, "capabilities", 0x0, "selabel", "u:object_r:system_file:s0");
set_metadata("/system/vendor/lib/egl", "uid", 0, "gid", 2000, "mode", 0755, "capabilities", 0x0, "selabel", "u:object_r:system_file:s0");
set_metadata_recursive("/system/vendor/lib/mediadrm", "uid", 0, "gid", 2000, "dmode", 0755, "fmode", 0644, "capabilities", 0x0, "selabel", "u:object_r:system_file:s0");
set_metadata("/system/vendor/lib/mediadrm/libmockdrmcryptoplugin.so", "uid", 0, "gid", 0, "mode", 0644, "capabilities", 0x0, "selabel", "u:object_r:system_file:s0");
set_metadata_recursive("/system/xbin", "uid", 0, "gid", 2000, "dmode", 0755, "fmode", 0755, "capabilities", 0x0, "selabel", "u:object_r:system_file:s0");
set_metadata("/system/xbin/librank", "uid", 0, "gid", 0, "mode", 06755, "capabilities", 0x0, "selabel", "u:object_r:system_file:s0");
set_metadata("/system/xbin/procmem", "uid", 0, "gid", 0, "mode", 06755, "capabilities", 0x0, "selabel", "u:object_r:system_file:s0");
set_metadata("/system/xbin/procrank", "uid", 0, "gid", 0, "mode", 06755, "capabilities", 0x0, "selabel", "u:object_r:system_file:s0");
show_progress(0.200000, 0);
show_progress(0.200000, 10);
package_extract_file("boot.img", "/dev/block/platform/msm_sdcc.1/by-name/boot");
show_progress(0.100000, 0);
unmount("/system");

also you must know that you have to restart recovery if you replace the file you're installing.

use adb sideload for better results