I've had similar issues with some versions of TWRP where flashing an Omni 4.4 nightly would leave me with no signal and an unknown IMEI. Flashing the very same ROM with CWM would work. (Odd, I know.)
FWIW I just flashed the latest t0lte Omni nightly with TWRP t0lte 184.108.40.206 earlier today and everything's been fine.
Another thing to look into is SELinux and making sure it is set to permissive.
My phones: Galaxy Note II SGH-T889V (with LTE enabled
/ ext4 SD card support on TouchWiz ROMs
), Motorola XT-1045 Moto G LTE (TWRP
Previous phones: Nexus S GT-I9020A, Galaxy Gio GT-S5660M (Arpeggiomod ROM
/ Discussion, stock rooted ROM
), Motorola XT-1032 Moto G.
Phones for which I play "tech support" for family and friends: Galaxy Nexus GT-I9250, Galaxy Q SGH-T589R, Galaxy 551 GT-I5510M, LG C-800G Eclypse, Motorola XT-1032 Moto G