As explained many times already on the forum, whenever you have double objects from default scenery popping out, it's NEVER a problem of the airport, and it's ALWAYS a problem caused by another AFCAD in conflict.
Use the free FSX Airport scanner program to find duplicates.
If that program doesn't find duplicates, that doesn't mean you don't have any. It only means that either the conflicting AFCAD couldn't be found by that program for some reason OR the conflicting scenery is not an AFCAD, just a generic .BGL.
In both cases, you'll have to search for the offending file manually.
The problem with AI bumping is likely caused by the same issue, if that offending scenery has a slightly different altitude.