Looks to be similar to my problem.
I'm on some unofficial CM10.2 and it has superuser integrated, so there's neither Superuser nor SuperSU app.
First I tried to restore backups I had on my Desire HD which was running CM10.1 - this failed horribly and resulted in every restored app crashing before even starting.
I thought there could be some problems restoring apps from another device but I've read it here: it shouldn't.
Even worse: backups that I make now on Nexus 4 result in the same disaster: after restoring data the app refuses to work, it just crashes over and over again. I do have SuperSU as flashable zip on my Nexus 4, but for this ROM I have not flashed it since there was superuser integrated :/
Should I better change the ROM? I don't even know where I found this unofficial CM10.2
And while we're at it: I've seen some "radios" for Nexus 4 and I suppose mine is still the one that came with JOP40C - is it necessary to flash a newer one? So far I haven't noticed any misbehaviour.
And to let it all out: on this unofficial CM10.2 I tried to change the "Minimum CPU frequence" because it seemed to me that 1026MHz is a little bit high for minimum. However, I change it and as soon as I leave the menu and return to it, the frequencies and the governor as well are the same as before.
What to do?