It might be time to just start over from scratch. Backup saved files and data (and confirm the data is safely archived and restorable), re-flash with the appropriate ROM, and do a Factory Reset -- the flashing replaces the operating system, the Reset wipes the user data partition. This returns the phone back to its original, first-time used state. And then it involves the arduous process of restoring your entire user account back to the way it was. But its current state sounds like there's a possible problem of a mismatch of firmware, along with a probable problem with 'root' status config files from miscellaneous apps you were using when the phone was rooted.