Thanks for that. 5.20.8 was used from about 6:30 pm on the 17th, so after the mdats you attached. For those mdats, my best guess is the 4 kHz start frequency for the sweep caused the auto window assignment to set a large left window (which I've fixed for the next build) which in turn triggered a bug with IR delay estimation and alignment that was fixed in V5.20.5, so I don't think the same issues seen in those measurements would occur in 5.20.8.
For the noisy/oscillatory-at-HF response that cleaned up after adding some timing offset I'd need to see mdats for both cases to comment further.
I think I've found what caused the null pointer exception you saw and fixed that for the next build.