I've had this problem a bunch of times. It just happens with the way they compress and convert the videos. Lot's of people on Vimeo have this problem, I read a couple threads about it in the Vimeo forums
Check out the Vimeo compression guidelines here:
...there's a section for audio. When I had that problem my audio was coming in at 48kHz and so I started using AAC to compress it to 44.1kHz. If you're in PP, you can do that as you export your video. I'm assuming this is the same for FCP/Vegas/etc as well.
Good luck, let us know if that helps. Cheers!