Might be a setting in the build that custom roms screw up. I just know for some time being on custom roms, my GPS is unable to lock on. But I screwed up 4.2.1 custom rom downgrade back to 4.1.X due to 4.2's profile architecture, so I ended up completely ODIN back to stock to start over. My GPS works again now and I went back to a custom rom and it still works.
Side question... regarding flash counter, I been doing some searching. Is this necessary? I understand if warranty work needs to be done, Samsung will reject the device if flash count is >0, but some ppl are complaining about having an unlocked bootloader with a unlock icon during boot. I don't have that?
Nexus 5 32GB Hammerhead on T-Mobile
ROM: Cataclysm ROM 12/06
KERNEL: Faux 005-mainline - uV -25
Nexus 7 32GB Flo
ROM: PAC 8/25/2013 Nightly