wait, so it happens only in a mission, or all the time, or ever since the mission?
the problem is, FSX isnt applying the alpha map to the trees.  why it would do it because  of a mission i dont know.  it woulndt be the Area51 shuttle mission would it?  those aliens can do some weird stuff 

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FS Water Configurator+ has new modifications in the works, plus DirectX 10, Service Pack
1, and Radeon HD 3+ Series support.