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These were taken with the QSI camera?
This looks like a shutter problem.
How many seconds were each flat frame?
I know that my QHY camera needs a good 2 seconds of exposure to not capture the shutter. Anything less and i get a darker bar down the side of an image.
You can check this by taking a flat file, then stretching it. If there is a black "bar" there then try increasing exposure time to over 2seconds. Is the black bar gone or still there?
If it is gone, make sure your ADU for the flats are OK. If it is too high then you will need to find some way to reduce the light coming in to the scope from your lightbox/source.
If the black bar is still there @ 2seconds,try 4 seconds. If it's still there, then you may have some vignetting caused by something (only other thing i can think of).
My first thought though would be the shutter.
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