When you created your backup via Philz/CWM did you make sure to set the nandroid settings to back up SE Linux context? if not that is probablye your issue.
* MK2/NAE ROMs * NAE Modem * 4.3/4.4 Kernels * MF9 Bootloader *

if you've found any of my blathering useful, there is a thanks button that can be hit.