Eric,
The issue I'm working to correct isn't connected to the rotator (although that does make things a bit more complicated), its the CMOS chip pattern noise that gets imprinted on flats if the exposure times for flats and flat darks are not matched. The time variation introduced by the skyflat routine make me need a different dark file for every flat frame. I would rather have all flat frames at same exposure time (matched exactly to a dark) and allow the stacking to handle the variance in lumination in each frame from the trilight sky.
I completed an experiment this evening and "tricked" the Sky flats routine into getting me a data set I need with a few frames I'll have to throw away. As I work up some examples I'll share in case anyone else acquires a CMOS sensor bringing these problems here.
This really isn't an ACP problem, its a new issue arising from very sensitive CMOS sensors with pattern noise.