I had this problem once and it turned out to be the orientation of the magnet. The sensor was detecting the magnet twice for each revolution of the wheel -- once for each pole of the magnet. I rotated the magnet 90 degrees and the issue went away. This might not be your problem but something easy to test.

Here's an article that explains this issue in more detail if anyone is interested:
Cyclometer Errors Caused by Magnet Orientation