Being rooted shouldn't matter. You can try backing them (your apps) up with mybackup or titanium backup, booting into revocery, wiping all your caches and factory data, and reflashing your ROM. Then restore apps one by one and see if one of them makes your phone act up.
That's the best I can think of right now, and it's time consuming but might be the only way to know for sure. Unless the ROM you are running has known issues that cause this (like maybe needing to update GAPPS or something like that).