Default [Q] mods disapear after reboot

Hi!!my problem is simple. I use an htc one xl with the custom rom CLEAN ROM 4.2.2. When i remove an app from the System App folder,it comes back after reboot and when i add an app in the System App folder it desapears after reboot,just like if the system auto restores every thing.Why deos it occur and how can i change it?? Thanks.