Well, Just to let you all know, I got .png's to work. I had some correspondence with Filip, and he told me that .png's and transparency were supported.
Transparency is definitely supported (both for PNG as for TGA), so I'm wondering if the problem is related to the drivers for your graphics card. Especially Windows Vista and Windows 7 are by default shipped with graphics drivers that have bad support for OpenGL (A:M supports both OpenGL and Direct3D, so it can be that A:M works fine already when it is set to Direct3D). But by installing a new driver from the NVidia or ATI site, the problem should be solved.
Did you also try letting 3DPainter create the transparent PNG or TGA texture (set background to 'transparent' in decal mapper)? If there's an incompatibility between Photoshop 6 and 3DPainter, that would show it.
I tried everything Filip suggested, but no luck.
What I ended up doing was downloading the super png plugin and installed into Photoshop. (I'm using vers 6). I deleted the original PS .png plugin. I created a new image with transparent background and then saved the image making sure to set the "Save Metadata" option.
Now when I place a decal in AM it is proper in AM and 3dpainter, and I can load the same image in 3dpainter using the bitmap tool and it is also proper, so needless to say I'm very happy.
Also just want to add Filip is very fast in his responses. I just reinstalled Windows and he got a new key back to me pronto.