Ha, I updated to LR 6.9 in hopes of I don't know what, but still nothing. Fortunately the command line works.
It's still weird to me that it's not actually going through each file when it says that they're not dual-iso, it goes way too fast. It's like there's a log file somewhere with bad data but I can't find mention of anything outside of the User\{user}\AppData\Local\Temp folder, but clearing that didn't do anything.