In both the new and classic theme, any large blocks of source code (eg Javadoc report for maven-xdoc-plugin) have sections of text missing in IE 6, and it appears/disappears depending on scrolling.
This must be something in maven-base.css that is incompatible (or perhaps in site.jsl itself).
This is likely an IE bug, but hopefully we can work around it.
This seems to be related: http://www.evolt.org/article/MSIE6_bug_with_floating_divs_and_spacers/17/23899/
I need someone using IE6 to test though...