There appears to be an issue with some matplotlib widgets that are packaged in py2exe where navigation button icons are not displayed. To remedy this problem, I changed icon file names in backend_qt4.py from .svg to .png. One clue to this problem was that one icon was showing, which was the subplots icon. In the function NavigationToolbar2QT._init_toolbar, it is the only icon using a png image.
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pelson commented on Jun 9, 2012
The qt4 backend now uses pngs for the toolbar images, so I assume this issue is resolved.