im using tgas with an alpha channel with no problem.
here is how I do the rendering:

glEnable(GL_BLEND);
glBlendFunc(GL_SRC_ALPHA,GL_ONE_MINUS_SRC_ALPHA);
glBindTexture(GL_TEXTURE_2D,tgatex[0]);
glColor3f(1.0f,1.0f,1.0f);


//rendering here

glDisable(GL_BLEND);

and the alpha channels appear transparent as it should be but the tgas are created by me so I know that they have the proper alpha channel.

World of Entaria|Shadowy Tree
Omnium rerum principia parva sunt.
Think twice before you code!!
Black Knight

Gotta love how you can overlook something so simple. I forgot to set the first component value in glTexImage2D to 4. I had it set to 3 for some reason. I now have holes in my cube, but the problem now is that I can still see a magenta edge around the box shaped gaps. Anyone know how to tell it not to blend the colors together like it want to do? If not then I''m going to have to use pitch black as my transparent color.