Make sure that you add the name of the model to the lights.rad, cause there are big areas of transparent polys on those trees, if you don't the whole poly is shading the leaves underneath rather than just the bit of the texture that is actually opaque. (for -textureshadows)
Then of course the obvious: run -staticproppolys and the vertex one I forget the name of. Make use of mat_fullbright 2 to see the actual shading with no texture to see if they ARE acting the strange way you think, or if they just LOOK like they are
Next on the tinker list: self shadowing for vertex lighting as earkham says
Then check normal maps (props don't use vertex lighting if they have a normal map...thanks valve)