David, I have been having the same problem as you, but today all worked for some unknown reason.
I have a qHY10 I was using on NGC7331 acquiring images with Nebulosity 3. I had a set of 20 light frame's, 50 dark frame's, 25 flats, 25 flat darks and a set of bias frames. All the lights, darks, flats and flat darks had pixel dimensions of 3896x2612, but my bias frames had 3894x2610. Very odd, all taken with same camera and pc. Today I tried a 0.001s exposure in lieu of a bias frame of 0.00s exposure. It gave the correct pixel dimensions. I then tried 0.0001s, it also gave the correct dimensions. For the hell of it, I repeated the 0.000s exposure..................... I got the correct dimensions. Why I got the correct dimensions today mystifies me, but all is well. As I have said elsewhere, as son as we get a PI image acquisition module the better!!!
Have you repeated the exercise to see if you get the same result?
Regards
Gordon