Comment 73 for bug 197163

Note - this is not an "official" Wolfram response, I just wanted to let you all know we're aware of the issues...

With that in mind, a few comments:

The original error messages are due to X11 providing an incorrect visual buffer to draw on - the 'export XLIB_SKIP_ARBG_VISUALS=1' command tells X to discard any composite visuals (which is what compiz and the like uses to do window effects) when we request a new visual. The reason we are getting a bad visual is complicated, but should be resolved by the next major release of Mathematica.

The extra windows are supposed to be hidden, and will go back into hiding with 6.0.3 (coming very soon).

The font rendering issues are related to Hardy's lack of some fonts we normally assume to be installed by default, namely a decent Courier and Times fonts. Some adjustments were made for 6.0.3, but if these do not resolve your issues, you may want to adjust the substitution rules (Option Inspector->Global Options->Menu Settings->FontSubstitutions) to point to fonts installed on your system.

On deleting/replacing libQt* - this is not recommended, as we ship a commercial version of the Qt library, which can potentially differ from the open source version. If it works for now, that's fortunate, but I would not consider that a permanent fix. We will be updating our shipping version of Qt with our next major release, most likely from the Qt 4 .3 version tree, as 4.4 is causing some compatibility issues (the above mentioned QObject warnings)

I'll be watching this thread if anyone has any additional questions or concerns, or you can email Tech Support (support.wolfram.com)

Jon