I think I have similar things happening...
My problems occured during the airport creation phases of the three I have done so far. Could it be that when one creates several layers of polygons, i.e. airport flatten, excludes, landclass base, landclass trees, landclass x, y, z... then when I load the scenery in sim sometimes I would "lose" the trees and the flattens went awry.
I discovered a small checkbox in ADE which says "Lock" in the layer properties.
So could it be that if you don't lock the layers before you post them as addons, then FSX chooses to layer the polys any which way but? Certainly now that I locked the hanglider pad layers things seem right. I did it for the paintshop airstrip too, so before Brad releases my addins, I'll re-send.