I saw something a while back that said that ML video capabilities would remain on someone's 50D even after uninstalling ML.
Have you tried removing both batteries?
Thanks for the suggestion, I hadn't tried that.
I removed both batteries for a while to reset everything, but there was no change in autofocus performance after.
I noticed that after I removed ML I could still record video, however this was fixed by removing the main battery.
I guess I'll check into having everything cleaned and hope for the best.
It would make sense that if the main sensor can get dirty that the auto focus sensor could too.
Hopefully the cleaning will help.