It's worthwhile buying a good polariser as some of the cheap ones are dire. They can cause distortion and colour casts. Also remember you will lose up to 2 stops through the filter so a tripod is recommended. If it's a genuine circular polariser it should work with AF but since less light gets through focusing can be tricky. Small apertures are ok but I tend not to go any lower than f16 as quality suffers - but thats probably for another thread.
I haven't used mine much ( a Hoya) but have never noticed a de-focussing effect. However, I always get a defocussing with my IR filter for the same reason James notes above and , of course, the difference in focal length due to wavelength. I suspect James is correct because at lower exposure levels you may be getting internal reflections off the inside of the filter that may throw the AF out of wack (just a wild guess). Try borrowing someone else's Hoya and see if it solves the problem.
Now to go and try out mine and see what happens!
Good luck with it
