I recently purchased a Canon 100-400mm L IS lens to use with my 5D MKII and have been using it trouble free off and on for a couple of weeks.  Today I was out shooting a marathon with it.  The shots were looking great but I decided to put a polarizer on the lens to cut down on some glare as the sun moved across the sky.  As soon as I did, the focus on all the images degraded dramatically.  I was shooting in shutter priority mode so the only camera setting that changed was the camera picked a more open aperture (typically from about f11 to about f5.6) to make up for the reduced light through the filter.

I've used this same filter on my usual lens (24-105 mm L IS) and never saw this issue with focus before.

As soon as I took the polarizer off the images came out perfectly sharp again.  I checked to make sure the filter was clean before I put it on the lens and I checked it again when I took it off.

I've never seen this type of behavior before.  Anybody have any ideas why this might happen?

Thanks!

I am just going to ask the obvious here:

Is it a circular polarizer?

What focus mode were you in? (ie al servo ai servo)

Did the focusing problem occur at all focal lengths?