Originally Posted by vndnguyen
Sorry I've never tried CM so I'm not sure what happens.
I have managed to solve the problem.
1. First back up EFS and FSG in case you haven't done that yet. On the N9005 your IMEI information is stored in FSG so do not use any tools that only backup the EFS without the FSG. For tools check here: http://forum.xda-developers.com/show....php?t=2611903
2. Flash stock image for N9005. I was still on JB 4.3 with the unlocked bootloader so I flashed JB 4.3 again, didn't bother with KK 4.4 which will lock the bootloader after flashing.
3. Booting back into stock and the SIM PIN entry menu appeared straight away.
4. Flash CWM recovery appropriate to your bootloader 4.3 or 4.4
5. Flash CM
6. SIM PIN entry and cellular works perfectly again
I'm not sure why this happened. Downgrading to a previous CM build did not solve the issue. So I'm reluctant to blame CM itself. Perhaps the recovery was the culprit. Somewhere something must have been corrupted during a flash. Luckily nothing that couldn't be fixed by flashing stock.