[Sony Cross-Device General] snurre:
I actually have the same problem with my Sony Xperia Z3, D6603.

Creating a zip with prfcreator 1.2, using stock FTF(D6603_23.4.A.1.264_1288-5531_R18C.ftf), SuperSU(UPDATE-SuperSU-v2.65-20151226141550.zip) and dualrecovery(Z3-lockeddualrecovery2.8.26-RELEASE.combined.zip). Including kernel/fotakernel/modem/ltalabel in the zip.

Flashing from TWRP is giving me error for kernel and fotakernel. Flashing only these two with flashtool afterwords, before booting to system, gets the phone up and running and everything works fine.

I have only tested prfcreator 1.2 with this ROM for now.

If anyone is interested in it, here is the part from my recovery.log which covers flashing of the ROM. SuperSU and recovery get installed just fine.

===========================================
| |
| *** Pre-Rooted Firmware *** |
| D6603_23.4.A.1.264_1288-5531_R18C |
| |
| Created with PRFCreator |
| by zxz0O0 |
| |
===========================================

Extracting files...
PRF is using sinflash
Installing firmware. This might take a while...
about to run program [/tmp/busybox] with 3 args
umount: can't umount /system: Invalid argument
run_program: child exited with status 1
about to run program [/tmp/sinflash] with 6 args
__bionic_open_tzdata: couldn't find any tzdata when looking for CST6CDT,M3.2.0,M11.1.0!
__bionic_open_tzdata: couldn't find any tzdata when looking for posixrules!
Flashing system.sin to /dev/block/mmcblk0p23. Please wait...
I:TWFunc::Set_Brightness: Setting brightness control to 5
I:TWFunc::Set_Brightness: Setting brightness control to 778
Finished
System flashed.
about to run program [/tmp/sinflash] with 6 args
__bionic_open_tzdata: couldn't find any tzdata when looking for CST6CDT,M3.2.0,M11.1.0!
__bionic_open_tzdata: couldn't find any tzdata when looking for posixrules!
Flashing ltalabel.sin to /dev/block/mmcblk0p18. Please wait...
Finished
about to run program [/tmp/sinflash] with 6 args
LTALabel flashed.
__bionic_open_tzdata: couldn't find any tzdata when looking for CST6CDT,M3.2.0,M11.1.0!
__bionic_open_tzdata: couldn't find any tzdata when looking for posixrules!
Flashing fotakernel.sin to /dev/block/mmcblk0p16. Please wait...
run_program: child terminated by signal 11
about to run program [/tmp/sinflash] with 6 args
Error flashing fotakernel.sin
__bionic_open_tzdata: couldn't find any tzdata when looking for CST6CDT,M3.2.0,M11.1.0!
__bionic_open_tzdata: couldn't find any tzdata when looking for posixrules!
Flashing boot.sin to /dev/block/mmcblk0p14. Please wait...
run_program: child terminated by signal 11
about to run program [/tmp/sinflash] with 6 args
Error flashing kernel.sin
__bionic_open_tzdata: couldn't find any tzdata when looking for CST6CDT,M3.2.0,M11.1.0!
__bionic_open_tzdata: couldn't find any tzdata when looking for posixrules!
Flashing amss_fsg.sin to /dev/block/mmcblk0p21. Please wait...
run_program: child terminated by signal 11
about to run program [/tmp/sinflash] with 4 args
Modem flashed.
__bionic_open_tzdata: couldn't find any tzdata when looking for CST6CDT,M3.2.0,M11.1.0!
__bionic_open_tzdata: couldn't find any tzdata when looking for posixrules!
Flashing amss_fs_1.sin to /dev/block/mmcblk0p19. Please wait...
Finished
about to run program [/tmp/sinflash] with 4 args
__bionic_open_tzdata: couldn't find any tzdata when looking for CST6CDT,M3.2.0,M11.1.0!
__bionic_open_tzdata: couldn't find any tzdata when looking for posixrules!
Flashing amss_fs_2.sin to /dev/block/mmcblk0p20. Please wait...
Finished
about to run program [/tmp/busybox] with 3 args
Cleaning up...
Finished!

For me it worked fine to just fix it with flashtool, so I'm not really asking for help. Just wanted to inform you of this, if it's any help.