Won't let me edit my post but, I've tried to set the Opacity for the whole image using the slider you suggested. I set it to 90 and the cloth hood that I had made still turned up as very reflective and shiny, I set it down to 5 and the hood was still shiny, set it somewhere in the middle and the hood still had the shine. Perhaps something is going wrong with the alpha layer?
http://img812.imageshack.us/img812/7677/hood3.jpg - now the texture looks how I want it to. I don't mind having to use the eraser but I assume after a while it will get tedious. Also can i recieve some feedback on what my texture looks like.
Weird! I wonder if it's just a bug in the DDS exporter? Or maybe the layer opacity isn't saved in the pixel data internally... Just to make sure that it's all straight-forward RGBA pixels rather than some kind of funky XCF internal format that keeps the RGB and alpha channels separate, try setting the opacity on the layer and then saving it out as a PNG. Reopen that try exporting again. If it's still shiny, then there's something strange about how GIMP handles layer opacity that makes it non-equivalent to an alpha channel.
Actually, perhaps 90% is just too little transparency to make a low-shininess specular map. Did you try setting it lower, such as to 50% or 20%? It should look as transparent as when you used the eraser.
As another way to get full-image opacity easily, you could add a layer mask and fill the mask with grey, which should make the layer translucent. After choosing "Apply alpha mask", this
should be exactly the same as if you'd used the eraser evenly over the whole image. If exporting that doesn't affect the shininess, then I'm at a loss for what GIMP is doing wrong!