Hey, I just recently discovered a solution to this problem myself. Here's a video that, among other things, shows the way to fix this:
https://www.youtube.com/watch?v=DbdwEo84nNoHere's a render with the eyes working (cycles render). I haven't tweaked it too much, but it's miles better than what it was.
*Edit: For the sake of posterity (in case the video goes down or whatever), I'll go ahead and describe the process.
First, make an alpha map of the texture you're using. The method shown in the video is to open the image up in the GIMP, and then:
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Image > Mode > Grayscale
Colors > Brightness-Contrast. Set Brightness all the way up (+127), Contrast all the way down (-127).
Colors > Brightness-Contrast again. This time, just turn the Contrast all the way up (+127).
Create a new layer, set it to all black.
Move new layer under first layer.
Now, export it to a new file and you're done. PNG, JPG are both acceptable, and probably TIF as well.
After that, you should have a total of three image textures to work with: your regular texture, your texture_ref (the sort of shiny, transparent gray one), and the new alpha texture. I've also attached a screenshot of the node layout used, which should be pretty self-explanatory.