Photoshop saves transparency differently than gimp when in TGA format.
If you have the actual texture item and are uploading it, just save it as a .png.
If you don't have the texture item and are going to place it in the custom folder, go to the channels palette, add a new channel (this will be the alpha channel) and then invert it. (Ctrl+i) Save as .tga, etc.
Either way should fix the problem.
If it doesn't try adding a second layer that is just 1 or 2 different colored pixels... just in case.