Hmm, forgot to mention that for the second try, I decided to have only the files in the iPod_control directory scanned. But it seems that I placed database.ignore in the root directory without any corresponding unignore files elsewhere...
After putting database.unignore in /iPod_control as I intended, everything works just fine

It's blazing fast too-- very satisfied user here!
I'll check my other files too and see if I can find any specific ones that cause crashes.
BTW, shouldn't "build database" do nothing in the case I described (ignore file in root directory)?