I had problems with transparent.gif images being posted with black backgrounds with wordpress 3.2.1 . I first figured out that when posting in thumbnail size it will give a black background. Using an image editor on my computer I sized my transparent image to the size I want it posted, upload the image to my wordpress gallery and then insert it as full size. It should turn out transparent. It did for me!
I also found this helpful post on wordpress.com help fourm.