I have a rooted Nexus 5, with TWRP recovery. I just got the OTA update. I downloaded it and installed it, but after the reboot my phone is still on 4.4.4. Any idea what's going on? Has this happened to anyone else?
Sure you can. You may not be able to apply an OTA update, but you can always flash the factory image. That's what I did to my Nexus 5, which had a custom ROM on it.