In Stacking Settings -> Intermediate Files, there are two options, but their outputs have been swapped:
• If you tick ONLY “Create a registered/calibrated file for each light frame”, it outputs the wrong thing: unaligned .cal files, instead of the aligned .reg files that it should produce.
• If you tick ONLY “Create a calibrated file for each light frame”, again it outputs the wrong thing: .reg files
• If you tick BOTH, then it outputs both types.
So this is not the correct behaviour for someone who only wants the .reg files and not the .cal files, or vice-versa.
It would have gone unnoticed (perhaps in previous versions too) if people wanted both.
Ray Butler reported this on the mailing list:
A bug I’ve encountered in 5.1.3:
In Stacking Settings -> Intermediate Files, there are two options, but their outputs have been swapped: • If you tick ONLY “Create a registered/calibrated file for each light frame”, it outputs the wrong thing: unaligned .cal files, instead of the aligned .reg files that it should produce. • If you tick ONLY “Create a calibrated file for each light frame”, again it outputs the wrong thing: .reg files • If you tick BOTH, then it outputs both types.
So this is not the correct behaviour for someone who only wants the .reg files and not the .cal files, or vice-versa. It would have gone unnoticed (perhaps in previous versions too) if people wanted both.