I'm pretty stumped. I wiped for new ROM and cleared Dalvik. I Flashed: Rom, APN, kernel cleaner, kernel (the new one you suggested), kernel cleaner. and its still doing the weird screen thing. I know you said that you do the new kernel after GApps, but since that's what seems to be causing the problem I flashed it this time. I'm up for trying leankernel.
Yeah, I'm a little baffled as well. The color issue was supposed to be resolved by any kernel build from after 10/20/2013, since that is when CM updated to fix their issue in their JellyBean nightlies. Anyway, here is leankernel for 4.3.x; if push really comes to shove, you can run stock kernel that comes with Carbon no problems, I just personally like the extra options that come with a custom kernel.
Dev-Host - lk_s3spr_aosp_mr2-v8.4.4.zip - The Ultimate Free File Hosting / File Sharing Service
Also, maybe this sequence:
Wipe for Install New ROM
Flash just ROM and APN fix
Boot to system, let settle
Boot back to recovery, flash just custom kernel (don't bother with GApps right now, we just want to see if the ROM/kernel combo works or not) after cache/Dalvik wipe
Boot back to system