Some rooting apps, like Kingroot, kingo, etc., install things and change things when they root the phone. That could be the problem, and the only "cure" is to back up everything, then reflash the ROM (unless it uses fastboot to flash - then the "-w" part of the script can be deleted and you don't have to back up, but I would just to have everything backed up - you can't recover anything from a phone that's been driven over).
As xocomaox asked, what make and model phone is it? (And please join the Android Central community, so you can keep the conversation here, instead of starting a new thread and explaining everything all over every time you post.)