Hi Tom,
My first thought is, "if you are using a cooled and temperature stabilised imager, why do you need to bother with Bias frames?". This thought then immediately raises the next thought, ". . . and, do you even need Dark frames (given that your exposure times are nice and short".
Of course, what you need to do is to evaluate the Bias and Dark frames that you did actually acquire. Perform a simple 'average only' integration on each subset (do not perform any form of 'calibration' on them). And then examine your 'Master Bias' and your 'Master Dark'.
What are the min and max range values for each? Use the STF sliders to 'zoom in' on the ADU values of interest - do you have failed pixels (hot, warm or cold)? If so, these are still better removed from images using a CosmeticCorrection approach, rather that trying to eliminate these in your Flats, and then having to repeat the process (pretty much identically) on your Lights.
Keep in mind why you are applying Flats in the first place - to eliminate optical issues such as dust donuts and vignetting shadows. You should really be able to even apply a Gaussian Blur to the Master Flat, and it should still be able to do its job.
== Modifications to orginal posting shwn in red ==A more insidious problem is how a colour imager 'sees' the light of your light box ( or skyflat, wallflat, etc.). More often than not, the imager will
not see a 'neutral grey' or 'white' source of light - it may
respond respond with a
Debayered image that has a significant colour cast - a much more predominant and obvious cast than when you use the same optical train on a Deep Sky object. As a result, your Flats can impose this colour cast onto each and every Light frame once you start calbrating. Not really what you want at all.
I prefer to adjust my Flats so that,
if DeBayered, they are as close to 'neutral grey' as I can get them
before I use them to calibrate any Lights.
I use a combination of an illuminated panel whose colour temperature can be adjusted to try and ensure neutral colour cast at the acquisition phase,
and a PixelMath process the new SplitCFA process that allows me to break the nonDeBayered Master Flat into four sub-images (one per CFA sensor colour) before adjusting the maximum ADU of each image, linearly, to a value of 1.0, (with no rescaling), then finally recombining these four new images back into the CFA channels that will minimise colour casts when this new image id uded as the Master Flat.Yes, it seems overkill - but we have long spells of non-imaging weather here, and I very rarely change my imaging train, so a set of Flats (and their assoiciated Master) actually have an extremely long lifespan
Hope this helps.