Update: I am loading several plugins. What I did to narrow it down was remove the plugins one by one until the error/self repair stopped. And it was on the Adobe Acrobat Pro XI package.
However... I tried it with ONLY the Acrobat package and everything is fine. It's a combination of 2 packages that causes the issue. Acrobat and a software called Vision. I'll be digging into it tomorrow and post my findings. This might help people with similar issues in the future... If I ever figure it out 