I can only confirm that duplicate buildings can only be caused by another scenery in conflict. The issue is, if it's an AFCAD, it's should be easy to find it, since there are tool made for that purpose, but if it's another generic .BGL, then you'll have to hunt it down manually.
Our provided exclude areas are made for the default KLAX but, if you have a modified one with objects in slightly different locations, we can't exclude them. And, we can't create an "universal" exclude file that would exclude everything in the airport area, it won't work because, due to a bug in FSX, if we did that, we would exclude our own jetways too.
