i have had a few similar problems, most recently it was due to changing my boot logos with the sn0wbreeze app, this caused my phone to always boot in safe mode but after a respring it was fine. I corrected this by NOR flashing the phone with sn0wbreeze firmware again and it solved the issue.
In the past i found the cydia app Quick SMS also caused this, maybe there was a conflict with another app i had but once i removed this, all was ok again
Hope this helps