OK, let me clear up a few things. I've caused this issue as posted in the OP. i fixed it by wiping data and reflash of the rom. I perfer not to do that again. this is likely not the last time i accidently cause this to happen as stated in later posts. I would rather find the piece of code or script i need to run to stop the bypassing of the lock screen.
@AqworldThunder you instructions are very vague. First, plugging the into the PC via USB brings up the SDcard content witch does not have system files on it. second, i used root explorer to look for anything on the phone called security, lock, reset, etc. I do not find anything in your talking about.
Let me say i know 1 way to fix this issue. Data wipe + reflash. I want to find another way. it was caused by apps, i dont see why it cant be repaired by an app/script.