GIMP :: Black Alpha Destroys Color Information

I have a texture for an object that will be rendered. The RGB for the texture contains diffuse color, and the Alpha channel contains a special parameter for the shader. The value for the parameter is 0 for 99% of the pixels.

In my XCF I have diffuse color on one layer, and the special parameter on another layer (as a greyscale).

So I copy the diffuse layer and call the copy Final. Then I create a layer mask on the parameter layer using the greyscale value. I copy the layer mask from the param layer to the Final layer, and then I apply the layer mask to Final, which should simply write the mask to alpha.

I look at the channels window to be sure, and alpha is written correctly, BUT everywhere that alpha is black THE OTHER THREE CHANNELS ARE ALSO BLACK! I can't fix this! What do I do? I even tried exporting to see if it carries through to the output image, and it does!

What's more, I tried to trick it by putting a very low value (like 1/2) in the pixels that are supposed to be 0 in alpha, and then I get an even weirder effect, wherein most of the color is kept, but some pixels color information is trashed anyway. Is there an export mode which will tell GIMP not to trash the color information on fully transparent pixels? Or better yet, can I tell it that alpha is not transparency?