Check how many types of speed tree you have on the route, I think once over 12 you can't place another type, to delete/place a tree check your in the route layer and running as admin. Trees don't disappear in 2010, 2012 SP 1 only.
The oddity is, I can add a TON of different ones in one editing session before they disappear (in the Objects window, not the layout itself). But last night, I did not add a single tree until I had done some work on the freight car workshop area in North Chicago, and the very first tree I tried to add at that time wouldn't let me. That, and the irritating flashing buildings (all built-in TRS10 ones, to boot), prove frustrating but at least there are workarounds.
Is that 12-tree limit the max you can put on the layout? Or just how many at a time?