Yup. In my case I had to make the entire centre of a_spellgembackground transparent where before it was just black (and thus usually transparent on most older TGA uses, but DBG decided to get all strict.)
You can do it with photoshop or gimp or whatever. Just look at the code in equi_castspellwnd.xml and see what .tga file is being referenced, and the x and y coords for the icon. Load it up in an editor, find the area, then make it transparent in the middle.
Same goes for a_spellgemhighlight (or whatever your .xml file calls it), needs to be transparent in the middle.
Worst case, for testing, you can copy the definitions from the equi_animations.xml file as placeholders so you can see where your particular problem lies. i.e. rem out whatever definition is in that spot and paste in:
Which is the spot in the newly modified window_pieces02 where DBG has their transparent spell gem background.