Uploading transparent PNG images to your profile causes the transparent colour to be made black.

I implemented a fix for this for Mahara today, maybe Moodle is interested in it too . Patch for Mahara is here:

http://git.catalyst.net.nz/gitweb?p=mahara.git;a=commitdiff;h=bfaa89d7ec77e2f47657783af277e78e6824a39a

I think your gdlib.php, function imagecopybicubic is what needs to be patched, but it's after midnight here and I don't know the moodle codebase so well, so will leave the details to someone else