Also, keep in mind that occasional floating buildings (autogen) is a known bug in FSX. It is random. Here is an excerpt from a Holger Sandmann post that talks about it:
The floating autogen houses are an unfortunate bug of FSX, or rather a side effect of how it loads terrain mesh and places autogen on it.
While flying in FSX the landscape components at mid to far distances are not loaded in full detail but rather at lower-resolution versions, often referred to as LODs or Level of Detail. Think of it as concentric rings of decreasing detail moving along with your aircraft. It's a common approach in games to keep frame rates at acceptable levels.
These lower-detail versions of data include the terrain mesh. Autogen trees and buildings are placed directly on top of this terrain, again a certain distance from the user aircraft (visible as the "popping-up" effect), and their elevation is fixed once placed. In mountainous terrain, especially in narrow valleys like at Skagway, the lower-detail terrain may have significantly different elevations than the highest-detail version. Thus, if the autogen gets placed while the lower-detail version is still being displayed then the autogen ends up in the air when the higher-detail terrain mesh replaces the lower-detail version. It's much more pronounced for buildings than trees because houses are placed in larger groups.
Unfortunately, there's no known fix for this, though perhaps choosing a LOD_RADIUS= parameter value in the fsx.cfg file may help with loading the higher-detail mesh sooner (I haven't tested this myself). A work-around is to refresh the scenery when you see floating buildings (you can set a key combination for that in the FSX Controls menu) but that is, of course, not a very satisfying solution.
In any case, any location with significant local terrain gradients is likely to suffer from this issue, anywhere on the FSX planet.
Rod