I posted this in the other thread already, so sorry for the dupe, but I hope this helps...
Kinda related to what Yogi Bear just said:
A few months ago, I was having a lot of issues with intermittent focus hunting on my 50D. There was no discernible pattern I could identify, and it happened with all three of my primes (28, 85, and 200). On the forum, someone suggested to look for debris on the focus screen; stating that the AF system somehow uses the focus points in the viewfinder to compute focal distance. (I still don't know if this is true or not) That said, I took a look through my viewfinder, and there was a big 'ole stinking hair cutting directly across the center focus point. Normally, I have a fair amount of debris inside the body because I change lenses quite a bit outdoors and I usually blow the body out every couple of weeks. So, having a hair in the viewfinder is something I usually disregard to the point where I don't even notice it anymore.
Anyways, I pulled the focus screen out. Blew on it, re-installed it, powered up, and camera was working properly again.
To this day, I'm not sure if the hair on the focus screen was actually the cause of the issue, or if it was just one of those "oddball" things that corrected itself or just my general ignorance.
Anyway, i hope my post helps.
It's good to know that resolves your problem. Thank you for sharing the experience. I bet there will be another person experiencing the same symptom, and looking for suggestion/solution. That's what makes this a great forum!

