I had no such problems in either my installs of 4.1.2, and yes I installed it twice.
Once I had fixed my N7 with a clean install of the factory image I got a notification of the update and applied it on my non-rooted N7, I then used the NRT to root and install TWRP recovery. Once I did this I backed up with TWRP and and restored my original stock ROM of 4.1.1 and used the update zip to update to 4.1.2, now I forgot to user Voodoo and lost root so used NRT again to root and install TWRP recovery...