Disabled app notifications getting automatically re-enabled
Here's the solution that worked for me. When 4.3 came out the first thing i did was place all my apps on the SD card which was great for freeing up space on the phone. Unfort. all app notification settings reset upon reboot as you described which was super frustrating. Specifically i'm talking about the app notification check box you see in every app when in android settings. I took 2 games in particular that kept waking me up at night with notifications and moved them back to phone storage which fixed the problem. Did 2 reboots in a row and it worked perfectly. Boxes are still unchecked

Hope this helps. 

Source : Android Central