I'm not sure, but it seems like rather than the areas outside of selection
being affected, not all of the selected area is becoming transparent. I used
the paint bucket (which is set to 100% opacity) to fill the selection in the
layer mask (which is acting as the alpha channel) with white. However, the
left-most column of the square selection was not completely transparent
in-game. It might just be something wrong with the game, because I looked at
the color values of the area I wanted to make completely transparent and they
are all 0,0,0. 

Thanks again for the alpha channel tips, I really appreciate it.

Also, I'm using .tga files. Maybe RLE compression has something to do with
this, but I always have it unchecked.

frustrated1 (via www.gimpusers.com)
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