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Using this markup in layout.master
<ul> etc etc <portal:SearchInput id="SearchInput1" LinkOnly="True" RenderAsListItem="true" runat="server" /> etc etc </ul>
<ul>
etc etc
<portal:SearchInput id="SearchInput1" LinkOnly="True" RenderAsListItem="true" runat="server" />
</ul>
this appears inside the rendered unordered list:
<div id='ctl00_SearchInput1_pnlS'class=''></div>
which is not valid markup within a UL and causes the site to fail W3C validation.
You can see the answer here
Thanks Aaron - good see this is fixed for the next release, and I've implemented a workaround successfully.