Warren,
I think that you are referring to the problem often seen with NB data. When you work with faint NB data, the signal level of the background can be quite low (particularly during new moon.) That means that when you do the flat correction, some pixels may be driven to have zero or negative values (after subtracting bias,) which PI clamps to zero. This can be caused by old bias data that may not provide sufficient offset to avoid having the data to cross into negative values when the flat correction calculation is done. Those zero values cause problems with the PI interpolation algorithm when you register the images. You'll know that you've run into this issue when you see a Moire pattern in the registered data. The problem is worse for images that require rotation and it looks like a 2D semi-rectangular or circular Moire pattern. The frequency of the Moire varies with the amount of rotation required. More rotation produces a higher spatial frequency pattern.
The fix for the problem is to add an offset to the calibrated data. If you look at the calibration dialog in PI, you'll see an option for "Output pedestal (DN)" under the "Output Files" tab. That's what that option does and that's why it's there. In this case, I had to add an additional 30 DN offset to the O3 and S2 signals to avoid this problem. Getting the offset adjusted to remove the zero pixel values completely fixes the problem. Just be sure to check the box to subtract the offsets when you stack the results. On possible side effect is that with an offset, the low-level statistical stacking filter can be affected and you may not reject data that would normally be tossed out. That may cause another side effect that seems to affect how local normalization data is computed. In that case, it may produce a very mottled background. Simply reverting to "additive with scaling" should solved that issue.
John