VERY hacky workaround for the Mathematica two extra windows bug:

1) Install compiz manager:

sudo apt-get install compizconfig-settings-manager

2) Run it via Settings -> Preferences -> Advanced Desktop Effects Settings
3) Make sure the Regular Expressions and Window Rules plugins are enabled
4) Go into Window Rules and enter the following in the 'Skip taskbar', 'Skip 
pager' and 'Below' fields:

name=XMathematica & !title=[A-Za-z0-9] & type=normal

This at least stops the windows taking up taskbar space. You can then
minimise the visual interference from each of these windows by holding
the alt key and rolling the mouse wheel down over the offending windows
to minimise their opacity, then drag them to the bottom of the screen.
They are now nearly invisible, behind everything and taking up no
taskbar space.

Alternatively, you can make the windows invisible by default by entering
General Options on the compiz manager, clicking the Opacity Settings tab
and clicking the Add button under window opacities, enter the same
name=XMath... string from above and setting the opacity to 0. This would
work nicely, except it means that you have invisible windows that you
can't 'click through' to access the desktop. Also, other windows making
the same name=XMath... statement will be invisible and will not appear,
though this is probably unlikely as the windows would have to match the
whole expression including not having a title.

Clearly a dirty hack but hopefully of some practical use anyway, I will
keep trying for a better method and post if any success.

-- 
Ubuntu 7.10: Mathematica and Matlab conflict with Compiz-fusion
https://bugs.launchpad.net/bugs/153045
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