Following up--for me, the goal was to find a folder icon that was "lightly" framed with a totally transparent or nearly transparent background. The default one with Glasklart was too dark for my tastes. I finally settled on the one that comes with the free theme Fifty Foot Shadows HD on Cydia. It's a super thin border though, so it overall looks smaller than other(regular) icons on the page. Still looking...Might have to make my own someday.
I wish all the transparent themes a) didn't have the stupid black icon issue and b) weren't so hard to make custom icons for. Yeah, I know I'm asking for a lot here. LOL But I'd use Glasklart or Fifty Foot in a heartbeat if I didn't have so many icons that don't fit the themes, and since removing the icon mask to fix the black box problem then screws with the unthemed icons, it seems there just isn't a great solution.
Sigh.