I hate to revisit a 4 month old thread but this was the most timely and the closest to what I just dealt with.
There are more than few transparent png fixer things on the web.. and they all attempt to work rather well until you run into a situation where you are using a script to generate the image and the png doesn't actually have a .png extension.
My solution for this was to use mod_rewrite to rewrite the image url so that I could embed a .png in a page the same way I would any static image. The result, for example, is that
myscript.php?image=bleh becomes bleh.png and all the fixes that look for .png find a .png
:)
Since I just dealt with this, I thought I would pass on that tidbit, should anyone else have similar trouble.