I have been taking new flats every time because I think my FW isn't putting the filters in exactly the same spot every time. It seems my vignetting is slightly different between filters. But it's been a few months, so I am just going off memory haha.
Dan - did you ever figure this out?
I am looking into my scope and it appears the filters are slightly misaligned to the chip, i can see the filter frame is causing vignetting