Second screen shot:
What makes you think the calibration refuses to apply the dark?
If I understand those screenshots correctly, scaling factors of around 0.94-0.95 are being applied to the dark. That is almost 1.0 i.e. very similar to a straightforward subtraction of the whole dark.
The bit to look for in the Process Console or the log file is where it mentions the dark scaling factor:
e.g.
Dark scaling factors:
t0 = 0.939
Mark
Because after calibration the subs are covered with the identical hot pixels which match up similarly to the dark master. When calibrated in CCDStack this does not occur. This behavior did not happen until after the first time I got this message a couple days ago: "** Warning: No correlation between the master dark and target frames" and those subs likewise were full of hot pixels as it is my understanding the master is ignored in such a case.
Now I don't get the warning and everything is as shown in my screen shots and the subs are not worth integrating after calibration. Yes I see what you mentioned about the scaling factors being applied but the results sure don't show it. After spending hours over two days doing this over and over I gave up and did the calibration in CCDStack. I don't remember having this issue with PI in the past until now.
Thanks for your response.