Grr! Don't you hate when you type something here and then after you decide to post you get something like "paa files cannot be attached" only to click back and see your entire message is gone!
Ah well. When I goto save the TGA as 32 bit I get an option to RLE Compress. Should I be doing this or not? I can save the TGA with Alpha Channels preserved, or so I think, because when I open it and run my cursor over the designated Alpha Chan area it disappears. But when I convert to paa (which I've attached below) and load up my addon, I get a solid black texture. Am I missing something here?
Also, I'm not quite sure I follow you on, "make sure that the right layers are showing" and when I tried to flatten I got a completely black image. Sorry about this, only just got Photoshop. Thanks for the help so far.