Aaaaahhh you mean to say that you are CHANGING FILTER from e.g. R to G!!! I thought you were rotating the filter wheel, i.e. the physical device, for balancing or so and then continued imaging with the filter that was previously selected.
OK, going back to the start: you need flats for every filter that you use. So if you use 8 filters, you need to shoot flats for all 8 filters, create master flats for each filter individually and apply those flats for the lights of the corresponding filter. If you do not do that then a dusk spec on, say, the R filter will (not may, WILL) become visible in all the images taken with other filters (G, B, Ha, OIII etc) when the R flat is applied to them.
Once again, the fact that this worked before is sheer luck. With all due respect but this is the first lesson learned when shooting multi-filter images and it is so basic that I honestly thought that you could not possibly mean that. Apparently I was wrong.