Sorry to hear about this, which version are you using?
Just to avoid assumptions: where do you open them? Do you open the PNG or the PS Touch project?
Does this only happen with images created in PS Touch? Have you tried to e.g. google transparenty png and adding it to the photo stream? Could you maybe add a screen shot of what you are seeing?
Well I sort of owe you guys an apology as it appears to be an iPad/iOS issue actually. Apparently I've never tried sending a transparent png to either my iPhone or iPad until learning/using Photoshop Touch (which I'm really enjoying btw).
But to answer your questions anyway, I was opening them on my iPad/iPhone in the Photos app and on my AppleTV in the Photostream there.
I made a quick transparent png from my Photoshop CS3 as well as downloading one from a Google search, all which had the same overlapping results.
I grabbed a screen shot for you, and blurred out the icons of images I think you'd rather not see ;-). Weird thing though too, which also points to this being an Apple issue, is that by accident, my first image, I saved as a png but with the background layer unlocked (being layer zero) and when I dragged it into this email, it overlaid the picture over the body of the email so that the black areas where transparent. So I dragged it out, resaved as a jpg but now I can't repeat the problem with the png, as I was going to create a screen shot of that for you as well. Either way, the icons on my desktop behave as normal and the images all open as normal. They all just get goofed up when displaying them in iOS as icons before actually opening the pictures.
So in this capture, there are six images with overlapping icons where the intended transparent png is on top of some random image pulled from the photostream.