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I just bumped into a wierd problem in all IE browsers and it turned out to be an HTML comment just before the DOCTYPE. The validator did not recognize it as an error but all IE browsers failed to properly assign css proeprties etc. This is not about the problem in IE but rather about the validator not showing the comment before the DOCTYPE as an error as it is an actual error.
In fact in both the HTML syntax (that is, documents served as text/html and processed by HTML parsers) and in the XHTML/XML syntax (that is, document served with an XML mime time and processed by XML parsers), a comment before the doctype is not an error. If any browser has a problem with such a comment, then the error in the browser, not in the validator.
I'm told this is a known issue in IE8 and previous versions of IE. Perhaps it's something they've fixed in IE9.