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As reported (tersely) in http://lists.w3.org/Archives/Public/www-validator-css/2008Feb/0016.html The CSS validator does not appear to follow <link rel="alternate stylesheet"...
test case at http://www.w3.org/QA/2008/02/altcss/altcss-sample.html looking into it.
Fixed in http://lists.w3.org/Archives/Public/www-validator-cvs/2008Feb/0116.html