Rooted Nexus 4 wants to update I got the problem that my Nexus sometimes wants to update to 4.2.1 although the system update menu says the newest version is installed (4.2). 

When I let the update do what it wants and it reboots, it fails at the recovery system with "apply patch check something".

Only thing I've done to my Nexus so far is rooting it.
I don't think a rooted Nexus 4 will be able to update automatically. So you might have to turn auto update off. Rooting will void its warranty. 

But not to worry, rooting is good. Some how you can flash an updated version of stock ROM manually to your device.