Comment 20 for bug 802690

LOL, should have looked at your screenshots :-(

Your "problem" has nothing to do with this question thread: that is about SikuliX using VNC.

You are simply running SikuliX on an Ubuntu machine as an interactive Jython session.
At the Jython level
capture()

starts an interactive capture.
So you have to paint the capture region.

... and the "black" area is part of the feature (the drawing pane).

That the screen image is offset by the left bar is a known glitch caused by the Ubuntu GUI manger.