Nick.
Not had the issues you describe creating Bias Masters with the Image Integration module in PixInsight and input data from a QSI683.
For a Bias Master I use typically 999 frames (maximum frames possible in PI’s II module) to create a manual “Super Bias” and do not use PI‘s ‘Super Bias‘ module which I find tends to generate inaccurate Master Bias frames with data from the QSI683.
Under Image Integration:
Combination = Average.
Normalization = No Normalization.
Weights = Don’t Care, All Weights = 1.
Disable (uncheck) Evaluate Noise.
Under Pixel Rejection (1):
Rejection Algorithm = Linear Fit Clipping (use if >20 frames, otherwise Winsorized Sigma Clipping for 10-20 frames or averaged Sigma Clipping for <10 frames).
Normalization = No Normalization.
Disable (un-check) Clip Low Range and Clip High Range.
Enable (check) Clip Low Pixels & Clip High Pixels.
Pixel Rejection (2).
All settings = Default.
Pixel Rejection (3).
All settings = Default.
Apply Global…..
With the above settings all my bias frames are accepted and the Super Bias Master created works as expected, the same settings should work with your data, selecting the appropriate Rejection Algorithm method in Pixel Rejection (1) according to the number of frames that you are combining.
If PI is still refusing to use all the frames then review the Process Console window after the Image Integration module completes for clues as to why it rejected your frames.
HTH.
William.