Does this happen if you enable the metacity compositor as well? It looks
like matlab is foolishly using an ARGB pixmap with full alpha set which
would work fine without compositing but gives the result shown when
things start caring about alpha.
To enable metacity compositing run gconf-editor and change the
/apps/metacity/general/compositing_enabled setting.
** Changed in: compiz (Ubuntu)
Status: New => Incomplete
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Problems with matlab when compiz is activated
https://bugs.launchpad.net/bugs/485792
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