the JPG file type does not support transparent backgrounds, converting to JPG will cause the transparency to turn black.
to maintain transparency, you will need to use PNG or GIF file types, unfortunately though, this only works on some transparent PNGS and not all.
we have found that some PNGs encode the transparency in a none standard format that cannot be detected by the GD library. This is a limitation of the GD library not being detect the non standard encoding.