Okay, so here's some progress (I think...
)
I tried making a new directory (ROMS Temp) that started off with the first 1,500 sets...
I was able to run a scan to the end (Having checked only the 'Sets' and 'Missing')
Upon completion, the expected results widow comes up, but is empty, and when attempting to redo the scan, all checkboxes are extremely slow to respond (I thought it had locked up again, but it appears that all processes are taking a minute or so to respond to mouse clicks)
I was eventually able to start a second scan (with all options enabled). The statistics window still comes up blank upon completion, but at least the scan went to 100%.
I'll have to do more testing tomorrow, once I get home from work, adding more files to see if there's some 'magic number' that causes the lockup, but in the meantime, I'd count this as progress!