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I have had problems with flats in the past. So yes it can suddenly go haywire when some simple step has been omitted or a few dodgy individual flats got into the master flat. I was playing around with some flats just last night to do with another thread and simple minor changes can make it go weirdly wrong.
Best to list exactly what steps you are taking and with what camera and scope, software and how you take your flats - dusk with a white cloth over the end of the scope, illuminated panel etc.
Its impossible to comment without knowing what your current procedure is.
Here at least is my procedure:
1. I take 6 to 12 flats at dusk or sometimes during the day with a white cloth cover over the end of my scope. In my case my observatory which is painted black on the inside walls lets in a small amount of light to make taking a flat possible. These work well. Otherwise I take dusk flats. It can be a race to take them and you need a camera with fairly fast download speed as you can see the ADU falling between subs. I increase the exposure length to compensate between filters.
2. I take bias perhaps 12 to 16 at the same temp.
3. Darks are about 16 subs and at the same temp and binning. I use sigma reject combine for the master dark using CCDstack. I do the same for bias.
4. Flats on a camera with a physical leaf type shutter like Apogee, FLI need a minimum of about 4 seconds exposure otherwise you see the shutter in the flat.
5. When applying to the same dark to the lights I do not use scaling but I tend to leave scaling on in CCDstack and bias subtract on.
6. I do median combine for flats and when applying the master flat to the images I check the subtract bias from the master flat. You can subtract the bias from the subexposure flats when making a master flat. I don't know it makes too much difference but for some reason I got better results doing it as I mentioned.
7. I check to see my luminance is flat fielded well with a trial and go hunting for what is different if I don't get a good result. I often do this while the camera is imaging so I've got something to do whilst I am waiting.
With a Sony sensor then you really don't need to do any of the above if your sensor and filters are clean which I prefer (of course before you start imaging). A bias subtract may be all that is needed unless you have dust donuts. So the above is the procedure for a Kodak sensor which are noisier and need the above to clean up. Or for a setup that has significant vignetting or dust donuts.
Is this similar to what you are doing? Do you scale your darks? Are you flats at a consistent ADU level more or less? I go for around 20-30K ADU. These work well. I have had some flats that seem too bright and get reverse to vignetting. I have had bad calibration when the darks do not match the lights precisely on temp and duration on some touchy scopes. Most though are fairly tolerant. Are you using 1x1 binned flats on 2x2 subexposures? I believe you can do that with CCDstack. I am unsure how well it works but perhaps.
I have at times used one flat from red for all RGB if I didn't get good flats for the others and the other coloured filters are clean with no dust donuts. Not ideal as perhaps they have dust donuts but if everything is clean I've gotten away with it. I usually have a separate master flat for each filter imaged with in exactly the same orientation as the filter wheel (perhaps not so important to match the orientation of the scope just the filter wheel and of course nothing changed in the optical train as well as the scope is focused and not way out of focus which could shift things.
The first thing I would do is check the master flat and make sure it looks like a usual flat that has worked for you over the years.
Greg.
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