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Hi Lewis,
I've never seen BPP crash when you don't have bias or darks. It normally just displays a warning which you can ignore. I've never seen complaints about overscan either unless you've been messing with the related parameters.
First I'd try clicking on the Reset button and starting from scratch. The second thing I'd try is doing a separate BPP run with just the flats to create a master before using it to calibrate the lights.
BTW, the use master boxes don't do what you seem to think. They just tell BPP that the first bias, dark or flat in each group is a master, not a single calibration file.
Cheers,
Rick.
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