Narrowed down the problem. It was due to CH PRO. Your latest update is not compatable. We will need a fix. Soon as I disabled CH Pro there was no further issues. So it was not an AFCAD issue after all.
This clearly indicates it's a CH Pro problem, which needs a CH Pro fix, since it's solved by disabling it.
Assuming you use the CH Pro version of the Zurich installer, there's no difference whatsoever between the two sceneries, except the CH Pro version doesn't have seasonal changes to match the fact that CH Pro doesn't have seasons, and has ugly green texture colors to match the CH Pro ugly green texture colors, but they are the same nonetheless.
Any altitude problems created by CH Pro, are something that should be fixed there, since our scenery uses the correct published altitude for the airport, and it surely can't change between the two version (standard or CH Pro).