Hi Roger,

Q1 - MaxIm does the calibration. So I'm not clear why it's necessary to copy the flats and calibration folders. If you haven't done this, try using MaxIm's Calibration Wizard (in the Process menu, and read the help file) to gather and generate the "masters" that can then be applied to each of your images automatically (if you've told ACP to apply calibration) without having to do the repeated copying of your flats, etc.

Q2 - It's a little hard to see but I think that your calibration images are not constructed correctly, because those kind of "defects" in an image should have been removed by calibration. I don't know if the real problem is an "offset" in the y-direction, but that's what it looks like to me. I did a little experiment once upon a time and generated fake flats with donuts to look at the impact of misalignment. Here are three tests of simple subtracting of FLAT2 donut from FLAT1, after offsetting one from the other. This is not too precise - just an illustration of what happens when the flat is not aligned correctly with the image. Here's a picture from the spreadsheet.

donuts.png

I tried to bring out the detail in your image, but you can see the similarity here. It helps to stand back from the screen some.
m81.png

I'll be the first to admit that this may not be the problem, but it is the first thing that came to mind when I saw your image.