Using a stock 12.04 AMD64 debian system I installed gnubg_0.9
+20120127-3 . Without the modification to the gnubg.desktop file it
fails as you describe. If I use a version with LIBOVERLAY_SCROLLBAR=0 it
functions properly.

This could be an environmental issue of some sort. First off where is
the gnubg.desktop file you are modifying? Is it the one in your user
directory or one in /usr/share/applications ?

When it runs (or you think it runs) with LIBOVERLAY_SCROLLBAR=0 how do
the scrollbars appear? Do they appear as standard scroll bars or do they
pop out at the edge as you pass over them? I'm asking this question
since how they will appear tells me whether LIBOVERLAY_SCROLLBAR=0 was
actually working.

What desktop environment do you use? Gnome3? Unity? KDE? etc?

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https://bugs.launchpad.net/bugs/1002063

Title:
  gnubg freezes desktop after analysing match

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