Hi Jared - I believe you may have nailed it. First, I did check the Auto Stretch feature at the same time I installed .16 as it had been turned off before. I did not think there was any connection with frames being skipped, so I did not mention it.
I installed 2.5.1.17 this morning and set a sequence of 500 bias frames running from my STL 6303 camera. So far I have generated 400+ frames with no crash at all, when previously I could not get past the second or third frame in a sequence. Better still there are no skipped frames or duplicates. I will run some more tests tonight, but it seems that Auto-Stretch bug was probably it.
Chris