When I first posted this the way I "fixed" it was to do a fresh install of Windows. Since then, I've only had this pop up once. From my experience, some Media Center plugins cause conflict with the DTBAddin. When I installed a Lottery plugin, the commercial skipping didn't work anymore. I restore back to before I installed and it worked fine. Installed again just to test and it stopped working again.
So with that, have you installed any new add ins lately?