Quote Originally Posted by Photo-John
This definitely seems weird - especially if it works with the 17-85mm zoom lens. Were you shooting in low light or did you have the problem in all lighting conditions?

There's used to be non-circular polarizers that wouldn't work with auto focus lenses. That would have been my first guess. Especially if its a cheap house brand filter. But the fact that it works with your other lens confuses the issue. However, most of us would encourage you to buy a better polarizer, anyway. The Canon EF 70-200 f/4L has about the best glass you can buy. If you put a cheap filter in front of it, you just compromised all that good glass you paid so much for. So the best solution might be to cough for a worthy filter. I usually paty about $100 for B+W polarizers. It's a lot of money. But they're built really well and you won't wonder if it's the filter anymore.
It was in sunny daylight, however on the canon forum someone suggested that the AF might not work properly with the CPL, just like using a X2 converter. Anyway I've just ordered a Hoya CPL, and tomorrow I'm taking some shots of birds of pray without the cheapo filter, so hopefully this explanation is on the mark.

Thanks for your reply

Balders