Ah, I should have known they would have been an issue, I'll see about maybe finding a way to 'scrub' these mods from the save file to see if I can get it to work, anyway if you think it can help here's the zip file containing the Imperator Mod and it's .mod file.
Thanks for the help so far!
EDIT: So, I've just noticed that while cleaning the save file that there are bits of land 'owned' by dead people and thusly they are unconquerable territory with no owner, and some of them don't have a duchy capital, only a 'building_type_' for its 'main holding'. I'm going to see about trying to fix that to.