I left out some of the info from my original post. The first time I returned the lens to Canon they confirmed it had a problem. Here is what they wrote on the service tag:
"...adjustment of the AF assembly was incorrect the auto focus did not operate properly. Electrical adjustments were carried out on the AF assembly."
When I got it back I checked it (with the filter in place) and found the problem still existed. I sent it back to them a second time and they replied with the same diagnosis and adjusted the AF assembly again. They also requested that, if I still had a problem, I send the camera body in with the lens.
The third time I sent both the lens and camera body (Rebel XT at the time). They again adjusted the AF and replaced the main board in the camera body ($212).
So, I sent it to them three times and they confirmed a problem with the lens' AF system three times. I never sent the filter with the lens. Pretty weird right? Maybe I should have thought to test it without the filter, but maybe you can also understand why I didn't consider it a possible cause - the Canon techs kept confirming focus problems and they never had the filter on the lens.
