We where not able to find a true fix for this person, it seams to be a problem with an earlier version of the free type library:
Unfortunately there seems to be an issue with the gd library and specifically
FreeType Version 2.3.7
where some .gif files will not retain transparency settings. We implemented a work around of setting the transparency color to white so that the issue isn't apparent on the site.
I think updating to a more recent freetype library may be the only way to truly solve the problem since I was unable to reproduce it with:
FreeType Version 2.3.9
Let us know if we can help with anything else.