Whose scenery (if anyone's) are you using? I am using MR's and UT's set up on a Rhumba mesh. My screenshots are taken on Marcus and MR's Guam (Orote). Marcus, seems to be no difference from stock except the new shorelines have made the island smaller. MR's Guam (Orote) is off a bit from the stock location in placement (I found myself next to a tree between 2 revetments on start). I took a dusk shot, just to show off the base's runway lights.
I'm pretty sure that if you are getting elevated objects on your terrain, and in those locations you definitely have some sort of conflict. Why don't you take a couple of screenshots of your Scenery Library under Settings and we can see what you have installed.