Why is this happening? It doesn't happen that often, but at some places the houses are always aloft. At one time trees were several hundred feet above the ground. I'm using the default mesh for this particular region, but an updated landclass. Is there anything I can do to fix this?

I had a similer problem with an add on scenery for Alaska. What fixed it for me was moving it's priority down in the scenery library, that paticuler add on is now 168 in the priority, originally it was 8. the defult alaska for me is 160 and 161.A few scenerys I cant fix that way, they are usually made with a terrain mesh that I'm not using (most of my mesh is defult ) but usually thats explained in the readme. So your problem could be that the scenery was made for a mesh other than the defult.Having FunGrey_Wolf

I sometimes get the floating trees too. What I do is pause the game first, then put the time compression up to 8x then back to the normal 1x time. FS2002 re-draws the whole scenery when it is put back 1x time and the trees are back to normal.