Well I can also confirm the problem with Hardy and Mathematica 6.0.1. 
I was waiting for the official release of Hardy to be launched, hoping that 
this bug would fixed by then - but it is still there. 

In my opinion this could NOT be a Mathematica problem, for the program
started to misbehave only after I updated from Gutsy. If Mathematica is
working with Gutsy flawlessly, it should also work with Hardy the same
way. BTW I am not using compiz at all and did also not change anything
(willingly) during upgrade.

Another observation is that Hardy release also brings another font bug
with its Gnome Terminal. Initially the Terminal comes detached from the
settings you are likely to make under Appearance/Fonts. Only after
changing settings in /etc/fonts/conf.d the previous (Gutsy) expected
functionality is restored.

-- 
Unable to input text to mathematica 6.0.1 in Hardy (regression from Gutsy)
https://bugs.launchpad.net/bugs/197163
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