I recently installed a 8 position filter wheel and had issue of the filter not lining up with the CCD window. The issue occurred randomly. If I power cycle the camera (disconnect the AC power, wait a few seconds and reconnect). It will fix the issue. Do you have any insight what the issue may be? The original 5 position filter has no such issue.
This may be a position sensor problem, or a problem with the belt. @Bill may have a couple of ideas on how to fix it, if possible. You can contact him at his email: bill (at) sbig (dot) com
There are several possibilities here, I think it would be best to have it come in for testing and evaluation. -Bill