Over the last couple of months I've been experiencing the same thing that the OP described with my Atik EFW2: SGP calls for a filter change and the FW reports it is "moving" even though the filter wheel has stopped on the correct filter. After a few minutes SGP will immediately abort the sequence. I should note that this EFW2 is about 5 years old and it has worked with SGP without issue that whole time.
This happened the first time I attempted a sequence last night right off the bat. Here is that log file. Without cutting power to the FW or any other equipment, I closed SGP and restarted SGP. When I connected the filter wheel it reported the correct filter and the sequence ran fine all night long (2 different imaging filters but changing to LUM for autofocus and meridian flip functions).
I've been trying to track this down for a couple of months now. The problem has occurred with different USB hubs and cables, so I doubt it's a communication problem. I've talked with Atik about this and they seem fairly convinced that I just need a new elastic band that goes around the internal filter disk. I don't know why that would make any difference, but Atik is sending me a replacement band. We'll see.
In the mean time I will also add a delay to see if that helps, but again I've had no problems with the FW and SGP for years until the last couple of months.