I think I know what the issue may be. In your original post, you said that you use the alpha channel out the transparent part in PS, and then save as a .png...
Photoshop has a funny way of handling things when it comes to .png's and alpha channels. If you're going to save as a .png, just make your background transparent instead of channeling it out (sounds like exorcism, hehe). If you're going to use the alpha channel, save it as a .tga or something else that can handle transparency.