right ok so your last image helps answer:
One thing I am wondering if SC can do - can you take an image using the region that's bigger than the dialog box, and then have SC automatically trim out the whitespace until it hits the borders, and then save only that as the screenshot? I always take the shot on white. That would work around the problem.
sc will do exactly this -- but what you are seeing is a side effect of CHILD windows on top of their parents -- this messes up SC's attempt to capture background transparency.
so the trick in such cases is to move that modal child window off of the main parent window before capture.
assuming you are following my logic, give that a try and let me know how it works.