And i can understand why it doesnt do that for png. Png is a format ment to be used as lossless compressed image format. If fully transparent pixels would still contain color information then those pixels are far more likely to take up extra space you wouldnt use. So a black or white background is more efficient.
Why TGA files get the same result i dont know since on those i actualy would expect the colors to be preserved. Especialy considering this is (or was) a popular format for textures within games.
However, i noticed that paint.net actualy does perfectly support the required format out of the box without any need of plugins. Save the image as DDS format, this is the format vtf uses. It will still compress the fully transparent area to be single color, but it will ensure that areas relevant to compression will retain its color information. No need for a plugin:
EDIT: after checking a few things with tumbolisu we noticed that paint.net does store the color information fine, but its vtfedit that compresses it again and messes up things. The DDS format is handled better by it, but that applies a compression a 2nd time and reduces quality.
Its probably better to use this instead:
http://nemesis.thewavelength.net/index.php?p=50
as directly converting is still the best way to go.
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