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Ok I think got the transparency working but now shadows on the object act all weird, any solution to this? (ps ignore the ugly unwrapping of the tree skin grin ):

I'd have to look at the alpha test / alpha blending setting. Also check your models normal

Also check when using flat polygons that these is no back-culling (like making a modeling software force 2-sided rendering).

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, yes this could be a possible alternative. The transparent leaves maybe can't give shadows, so the tree would have to have some dummy leaves for shadows or a alpha layer / png skin for shadows. Maybe I just create real 3d leaves for the model.

In shade-c checking the ents flag1 turns off it's shadows ( Just fyi)
Transparent leaves and simple plains with alpha to fake leaves should cast shadows fine. Again check if you are turning off backface-culling.

My notes are from my use of Slin's improved PSSM so I may be wrong for the shade-c version.