I did have one of the alternate proficiencies installed. It wasn't the IWD one, it was one of the options similar to original BG, with the broader weapon groups.
Ok, so I deleted my original debug logs, uninstalled all the option from the randomizer mod, and ran it again with --debug-assign and --debug-value. But this time it went through, (somehow, despite having failed dozens of times with these exact same options before), and now I can't uninstall it again. Every time I try to run it, it jumps to asking me what mode I want, with the messages about skipping the randomization options