We found a solution that circumvents the maintainability problem by specifying the image path in the xhtml source (uses the default $wgLogo now).
The png fix function is switched on again but needs some improvement: In some versions of IE6 with some security configurations it pops up ActiveX warnings which is highly annoying.
Finding a way to detect ActiveX would be a cool small project for somebody with ie/js skills. The file to hack is http://test.wikipedia.org/style/IEFixes.js. Fixalpha should only fire if the filter is allowed to execute.
Any takers?