sreilly, I had exactly the same problem as you describe, just a few days ago (which I reported here).
I am not 100% sure how this happened, it was probably related to the reinstallation of PI and deleting my old config files.
Anyway after deleting all my FITS images and converting RAWs once more to FITS (this time making sure they all were 32-bit floats) everything worked as usual. I suspect one of my calibration images (probably the bias ?) was not 32-bit causing the effect you mention. Please note that you can not detect this by just opening the calibration files and looking at them in PI; they looked all OK in my case, which doesn't mean that they fit together. You might find out which one is causing the trouble by excluding it from the calibration process and re-calibrate your images or you might check the properties of the images.
Clear skies
Tahir