OK, now i need some more Infos.
For what do you need the alphacannel (32bit)?
Do you apply a Shader to your terrain?

If you don`t use a shader you will always have this problems with opaque portions sometimes look transparent. If a Skin have 32 bit then the engine will render the Terrain at the transparent pass and that gives problems.

maybee that can help:
set the flag PASS_SOLID in the Material of your terrain.