I'm not sure if this was the intended effect but after trying the Alpha spec feature within 3DS, I had to redo the alpha masks manually since it would bake the specular into the RGB channels as well as the alpha of the Normal.
Here is an image of the problem, showing just the RGB without alpha in VTFedit
The specular had noise added to it from CrazyBump so I don't know if that was apart of it that caused this to happen.
In 3DS, I had the Gamma options disabled, not sure if that played a part.
I was originally going to attach the image but the max file size is 512KB, is this due to the space on the forum server? It's kind of impossible to get an image below 512KB for upload.