I'd like to bring this thread up to speed from the SGP forum. It appears at least a few other people are experiencing the same issue.
I have been in contact with Vince about this and he has been very responsive. I'm waiting on a new filter wheel elastic band from Atik.
In the meantime, one "fix" that seemed to at least cut down on the frequency of the problem was to set a filter delay in SGP that basically pauses everything for xxx seconds after a filter wheel move.
Even so, after several nights of imaging were interrupted by this problem, I reverted back to the old core software (the pre-July 5 drivers) and since then I have had two full nights of imaging with SGP changing the filter after each exposure, so the EFW2 is getting a workout. The problem is so random that this could just be coincidence, but so far the old core software seems to work well.