I don't seem to recall having that problem when I did my 205 skins.
However, it is definitely doing it now. Perhaps a recent bug, introduced in a later patch?
I did get a workaround running, though:
You don't need to play with the file's alpha layer in the .txt, just leave that as-is. Right-click the art bitmap, hit "edit" (which will load MS paint), eye dropper the purple alpha color, then select all (ctrl a) then delete, then color fill the purple you previously selected back into the area. Save file, close, and you're good to go.
I say MS Paint because it won't re-save the indexing of the colors, and you can leave the alpha txt file as-is. If you open in photoshop, and it re-saves the color indexing, you have to find out which color is the right one to enter into the .txt and my way just avoids that.