I have no idea at all! Actually thats pretty odd, I would think that a magnet anywhere near an electrical circuit would cause mayhem! I don't suggest removing though, its probably there for a reason.
Have you tried installing the fan then re fitting the cover? Maybe the cover needs to be on so it can work or something.
I found a video you could check out, if it doesn't solve your problem maybe you could clean up you old fan and re-install it. Check it out, it may be helpful:http://www.youtube.com/watch?v=m9H2K9IGWj4