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I grabbed a freehand region and selected copy then pasted it into word. The image was not transparent but got a black square arount the image it self.
Have you try the option (preferences->snapshot) "force background color for clipboard/web services" ?
The transparency aren't well supported into clipboard in many tools ...
Yes, but that only changed the "black" part to white.
And ? If transparency in clipboard isn't well supported by your program, I'm not responsible ... If you save the snapshot as a normal png, you can get the "normal" transparency. On windows, I've try with XNView (good result) and Photoshop (bad result). I don't see what I can do .. or I've not understood your problem.