I'm not sure, if I understand your problem entirely; I'm not a big fan of addons, so I don't download any addon I see, so I don't have such problems. So I'm not sure, if I can help you, but that's how I would do:
firstly, I'll take a pill to calm down myself, then I'll devide the map on sectors, then I'll copy and paste the sectors on new, clean map, and check, if the error msg shows up. I'll repeat the procedure, until I'll find the sector, which gives me the pain. Then, if possible, I'll delete the sector, or I'll devide the sector on sectors, and... Or I'll even delete the whole (and when I say whole, I mean WHOLE) map, and in those three days I'll made a new intro.
And there're no such things as a noob problems, there're just ... problems.