That doesn't sound very encouraging. I will have to see if I can pin down the problem myself, because the default scenery problem vanishes when I disable Scotflight Photo in the Scenery Menu. Unfortunately, I can't recall whether the "invisible house" problem existed before installing Version 2.5. However, I know for certain that the default scenery problem did not exist with Scotflight Version 2.4. I visited the Archerfield Estate airfield very recently, and I would have noticed it.
I am not aware of any other problems, so I am reluctant to go down the "reinstall FSX" route without further investigation.