Really quick solution (VS2005) - check the "ZOrder" attribute of the DataSets in the underlying .xss file.
I had the same problem, but only when I opened one of the XSD designers in Visual Studio. All the others worked fine.
I found out that 2 of my DataSet Shapes had the same "ZOrder" value ("2") when I opened the XSS file:-
<DiagramLayout xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:xsd="http://www.w3.org/2001/XMLSchema" ex:showrelationlabel="False" ViewPortX="7" ViewPortY="15" xmlns:ex="urn:schemas-microsoft-com:xml-msdatasource-layout-extended" xmlns="urn:schemas-microsoft-com:xml-msdatasource-layout">
<Shapes>
<Shape ID="DesignTable:DataTable1"ZOrder="2" X="26" Y="44" Height="827" Width="258" AdapterExpanded="true" DataTableExpanded="true" OldAdapterHeight="0" OldDataTableHeight="0" SplitterPosition="823" />
<Shape ID="DesignTable:DataTable2" ZOrder="2" X="704" Y="458" Height="130" Width="204" AdapterExpanded="true" DataTableExpanded="true" OldAdapterHeight="0" OldDataTableHeight="0" SplitterPosition="126" />
</Shapes>
<Connectors />
</DiagramLayout>
I made them different (set one of them to "1", kept the other one as "2") and the DataSet was immediately editable in the designer.
Hurray!