I'm seeing this problem with pango text drawn on top of a picture. Instead of transparent parts being from the picture, the background of the text is a box, probably of the color that is actually background of the picture.
All versions of gtk+ since (and including) 2.24.21 are affected. I've tested a build with patch from bug #695636 (gone in between 2.24.20 and 2.24.21) reverted, and that build works ok. Many other people seem to have reported similar problems to that bug since it has been closed.
My gut feeling would be to revert bug #695636, but that's based mainly on the fact that the ticket does not list any cases where the bug has ever caused actual problems for anyone whereas the fix has been reported faulty many times.

Downstream (freeciv) ticket, including screenshots and other data: http://gna.org/bugs/index.php?21475