Quote: "I can't figure out how to make the alpha channels and I don't know how to make a specular map. I think that will fix the problem."
If you have Photoshop you can view channels in botton right corner using the same tool as the layers are in.
Specular map needs to be Gray Image but still (RGB/8) and add a 5th channel using the tool in the bottom right... this new channel added will automatically be alpha.. click the properties of this channel... make sure its color is black and its 50% transparent...
TIP: you can take areas in your specular map that you want to be Shiny and make then Whiter in the gray scale part of the map... this well make the light shine off them more.... If you want Areas to appear lit you need to add white or gray to the Alpha channel.. which well make them lit even with 0 Ambiance ( IE Small lights etc on the wall/object.)
Hope this helps
Squalker