Found the fix ! You need to rename the following file to .off, and then a standard exclude on the AFCAD will do the trick to get rid of generic buildings.
C:\Program Files\Lockheed Martin\Prepar3D v5\Scenery\0702\scenery\cvx6122.bgl
I think OTHH wasn't included in P3Dv4/v4.5 and now is, and the CVX is messing things up.