[HTC One X] Daekin:
I did not change permissions manually. I have fixed updater-script as follows:

Removed red lines here

if file_getprop("/tmp/aroma-data/tweaks.prop","item.0.2") == "1" then
ui_print(">>> Installing OpenVPN Support");
package_extract_dir("common/aroma/tweaks/openvpn", "/system");
[COLOR="Red"]symlink("/system/xbin/ifconfig","/system/xbin/bb/ifconfig");
symlink("/system/xbin/route","/system/xbin/bb/route");
set_perm(1000, 1000, 0755, "/system/xbin/openvpn");[/COLOR]
endif;

if file_getprop("/tmp/aroma-data/tweaks.prop","item.0.3") == "1" then
ui_print(">>> Installing SQLite Tweaks");
package_extract_dir("common/aroma/tweaks/sqlite", "/system");
[COLOR="red"]set_perm(0, 0, 04755, "/system/xbin/sqlite3");[/COLOR]
endif;

Added green lines here

ui_print(">>> Creating additional symlinks");
set_progress(0.85);
symlink("/system/bin/mksh", "/system/bin/sh");
symlink("/system/fonts/Roboto-Regular.ttf","/system/fonts/DroidSans.ttf");
symlink("/system/fonts/Roboto-Bold.ttf","/system/fonts/DroidSans-Bold.ttf");
[COLOR="Green"]if file_getprop("/tmp/aroma-data/tweaks.prop","item.0.2") == "1" then
symlink("/system/xbin/ifconfig","/system/xbin/bb/ifconfig");
symlink("/system/xbin/route","/system/xbin/bb/route");
endif;[/COLOR]
ui_print("");
ui_print("");

and here

ui_print(">>> Setting permissions");
set_progress(0.95);
set_perm_recursive(0, 0, 0755, 0644, "/system");
set_perm_recursive(0, 2000, 0755, 0755, "/system/bin");
set_perm(0, 3003, 02750, "/system/bin/netcfg");
set_perm(0, 3004, 02755, "/system/bin/ping");
set_perm(0, 2000, 06750, "/system/bin/run-as");
set_perm(1002, 1002, 0440, "/system/etc/dbus.conf");
set_perm(1014, 2000, 0550, "/system/etc/dhcpcd/dhcpcd-run-hooks");
set_perm(1000, 3003, 0640, "/system/etc/gps.conf");
set_perm(0, 0, 0555, "/system/etc/init.post_boot.sh");
set_perm(0, 0, 0400, "/system/etc/hsml.key");
set_perm_recursive(0, 0, 0755, 0555, "/system/etc/ppp");
[COLOR="DarkGreen"]set_perm_recursive(0, 2000, 0755, 0755, "/system/etc/init.d");
set_perm(0, 0, 0755, "/system/etc/init.d");[/COLOR]
set_perm_recursive(0, 2000, 0755, 0644, "/system/vendor");
set_perm(0, 0, 0644, "/system/vendor/firmware/libpn544_fw.so");
set_perm_recursive(0, 0, 0755, 0644, "/system/vendor/lib");
set_perm(0, 2000, 0755, "/system/vendor/lib");
set_perm_recursive(0, 2000, 0755, 0644, "/system/vendor/lib/drm");
set_perm(0, 0, 0644, "/system/vendor/lib/drm/libdrmwvmplugin.so");
set_perm(0, 0, 0644, "/system/vendor/pittpatt/models/detection/multi_pose_face_landmark_detectors.7/left_eye-y0-yi45-p0-pi45-r0-ri20.lg_32/full_model.bin");
set_perm(0, 0, 0644, "/system/vendor/pittpatt/models/detection/multi_pose_face_landmark_detectors.7/nose_base-y0-yi45-p0-pi45-r0-ri20.lg_32/full_model.bin");
set_perm(0, 0, 0644, "/system/vendor/pittpatt/models/detection/multi_pose_face_landmark_detectors.7/right_eye-y0-yi45-p0-pi45-r0-ri20.lg_32-2/full_model.bin");
set_perm(0, 0, 0644, "/system/vendor/pittpatt/models/detection/yaw_roll_face_detectors.6/head-y0-yi45-p0-pi45-r0-ri30.4a-v24/full_model.bin");
set_perm(0, 0, 0644, "/system/vendor/pittpatt/models/detection/yaw_roll_face_detectors.6/head-y0-yi45-p0-pi45-rn30-ri30.5-v24/full_model.bin");
set_perm(0, 0, 0644, "/system/vendor/pittpatt/models/detection/yaw_roll_face_detectors.6/head-y0-yi45-p0-pi45-rp30-ri30.5-v24/full_model.bin");
set_perm(0, 0, 0644, "/system/vendor/pittpatt/models/recognition/face.face.y0-y0-22-b-N/full_model.bin");
set_perm_recursive(0, 2000, 0755, 0755, "/system/xbin");
set_perm(0, 0, 06755, "/system/xbin/su");
set_perm(1000, 1000, 0755, "/system/xbin/sysro");
set_perm(1000, 1000, 0755, "/system/xbin/sysrw");
[COLOR="green"]if file_getprop("/tmp/aroma-data/tweaks.prop","item.0.2") == "1" then
set_perm(1000, 1000, 0755, "/system/xbin/openvpn");
endif;
if file_getprop("/tmp/aroma-data/tweaks.prop","item.0.3") == "1" then
set_perm(0, 0, 04755, "/system/xbin/sqlite3");
endif;[/COLOR]
set_perm(1000, 1000, 0771, "/data");
set_perm_recursive(1000, 1000, 0771, 0644, "/data/app");
ui_print("");
ui_print("");