I opened a bug in the compiz fusion forums regarding the issue, this is
what a member replied:

"gnome-screenshot relies on finding the parent window containing the
currently focused widget, then the parent of that, and the parent of
that, all the way up to the top level, where it is presumed that the
parent just before reaching the desktop window is the window border.
Since the window borders drawn by Compiz's window decorators aren't
actually part of the window, the last parent that gnome-screenshot sees
before hitting the desktop window is the focused window, minus the
borders.

Compiz plugins know offhand the exact size and position of every window,
so they don't need to look for parents, and don't encounter the same
problem.

... That's as much sense as I was able to make from the source code,
anyway. *shrug* What I mean is, even though it may seem like an easy
problem to fix, it may not be."

http://forum.compiz-fusion.org/showthread.php?t=4957

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Taking screenshots of the invidual window fails to capture window decorators
https://bugs.launchpad.net/bugs/74008
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