When I save out a 32-bit TGA from Paint.NET, the alpha channel appears to be stamped into the RGB channels as well. You can see this in Photoshop when you load the file back in: if you look at the RGB channels only they have been made black where the alpha was zero.
Although for most purposes I'm sure this is fine, it's a MASSIVE ball-ache for the project I'm working on, for a number of reasons. For one thing, I can't just turn off alpha blending and re-use the texture as a solid fill in my renderer, and there are other workflow related problems it causes.
The only reason I can think of for doing this is to improve RLE compression. If you could possibly, possibly find the time to make it optional in a forthcoming release...
