(At the risk of saying little helpful) I don't think that simple material has anything to do with it. Shouldn't you use the model material and then change those members at runtime in the entity action. maybe not.

Edit* are 60 trees in scene at once? (sorry if I miss understood)

Didn't you post that the ent_geometry was the thing that stats panels showed increased when looking ~long. Could you give as much info about what is in the scene at time the frame rate drops. All info you can give helps.

Some thing of note -

Many running functions.
First load of entities.
Jump from no scene to many entities in scene.
No LOD
Big clip ranges
Some shaders
Crazy big textures
Not using chunked terrain.
Not using a terrain shader.
Using extremely high poly count models and poor LOD steps.

I hope that helps. I really don't know much here.