For those that may not have figured it out. On AOKP especially, but some other ROMs have SDM.apk in /system/app . It is Samsung's Download Manager, or something like that. It is supposed to help with OTAs, since you are rooted and ROM'd it isn't necessary and can safely be frozen, renamed, deleted, moved, or whatever.
Of course there are potentially more things that can hinder your device from deep sleeping, but on AOKP that is one of the big ones. So I could be wrong, but since there isn't a lot of info here about AOKP, I figured I would post this just incase someone has the same problem.
Side note, I think it is going to be left off in the next build, as the developer asked if folks wanted it or not. General consensus seemed to be to axe it from the next build.