Hi Tim,
The only problem with these data is dark frame optimization. Disable it and everything works correctly (well, your flats are not correcting well near the bottom border of the image, and with just three dark frames you are introducing a lot of noise, but these are different topics).
The dark frame optimization algorithm cannot work correctly without bias subtraction. Since you don't have bias frames, you must disable it in BPP (also in ImageCalibration if you are preprocessing manually). Consider acquiring bias frames—they are cheap, you can take lots of them in almost no time.
