I have a GN that was bought in HK so it had a slightly different ICS build that would stop OTA updates. I flashed the standard takju build to it and then rooted it. That enabled me to get the 4.04 update OTA.
This morning I was pleasantly surprised to see a notification that 4.1 JB was waiting so I agreed and started the update. Unfortunately on the reboot I saw the Android character with a red exclamation mark over his stomach! Not good. It turns out that the OTA 4.1 won't work if you're rooted. Luckily I was ale to remove the battery and restart the phone back to ICS 4.04.
Turns out the only way for me to get 4,1 OTA is to flash back an original Google firmware image and return the unit to stock. Then wait for JB and then root it.
A nuisance since the GB has no SD card so I have to backup the entire phone before I am able to do that.