You're not using reference shaders somewhere in the list are you? I've found on occasion some peculiarities with how alpha or transparancy handles things in those instances. (Seems to be a bug in versions 5 & 6.) Instead of using the references, you actually have to copy and paste settings over from the other shader. In my case I discovered it since it was a pain in the butt trying to figure out why a shader based decal wouldn't apply properly.

It could also be one of the texture map settings, I'd play with the premultiplied or color/alpha toggles. Sometimes alpha or transparency seems to work better with .tga or .png images that have actual alpha to it.

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Barbequed Pixels?

Your friendly neighborhood Wings3D nut.
Also feel free to browse my freebies at ShareCG.
There might be something worth downloading.