IDK, but when I save 32-bit transparent images in PDN, they end up not showing any transparency in certain applications. Such as in the case when I edited sprites from Angry Birds. As a test I drew up a squiggle on a transparent background, and then saved it as a 32-bit PNG. Then I replaced one of the ingame sprites (the birds sheet to be specific) and fired up the game, and it ended up something similar to this:
As you may notice you can see what appears to be a white bounding box of sorts:
This is what the test sprites look like when I use 3.5.8:
Downgrading to 3.5.8 does the trick as a workaround, and as for trying any plugins, no I haven't yet. I also took a peek at the images in TweakPNG, and from what I can observe, the latest version adds a white background to the image when viewed in TweakPNG's image viewer, while v3.5.8 douses it in black. A similar issue also happens in Photoshop; I'm not sure as to why but it does save properly in certain other applications besides PDN.
Oh, and here's a rar file with the sample images I made using the two versions:
http://www.mediafire.com/?vcj2a5qr1jqc4sl