Thanks for your bug report. Is the issue you describe by any chance related to http://bugzilla.gnome.org/show_bug.cgi?id=333737 ?
** Changed in: pygtk python2.4-gtk2 (Ubuntu)
Assignee: (unassigned) => Ubuntu Desktop Bugs
Status: Unconfirmed => Confirmed
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pygtk init modifies sys.path
https://launchpad.net/malone/bugs/39035