Transparency and color black

Anyone else experiencing some "weirdness" with the transparency? When I create a .png, containing black, and some transparency. When I upload it into my game engine, it reads the transparent as "black". When I open the .png in Paint.net, it seems okay, so I figure its just has something to do with how the game engine is rendering images from pyxel. Its strange because it doesn't do the same thing from other editors. If I highlight the transparent in Paint.net, and erase it, then export, it acts like it should.  That probably didn't make any sense, and I apologize. It's just disappointing.
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