I am assuming that it is happening with one runway, and not all. MS has screwed up some airports. For example, I seem to recall and airport in Bulgaria that has a VOR antenna in the middle of a taxiway.
If it is only a couple of airports that are a problem, I would suggest searching Avsim's library for scenery/afcad upgrades to those airports.
If it has happened to a lot of airports, then please list any scenery upgrades you have already installed. Maybe we can figure out what moved the trees.
Of course, if you installed no upgrades and trees are growing out of all your runways, I'd suggest putting your FS on ebay and watch the tree huggers pay a lot of money for it.
I hope it is understood that last suggestion is supposed to be humorous.
CEO, Omega-Air Virtual airlines