I changed the doctype to <!DOCTYPE XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
and everything in IE started lining up!
For anyone using DotNetNuke's hosting software, this solution worked for me:
Create an XML file named after your loaded skin, like this:
Inside, place the doctype you want, escaping out the characters...
<![CDATA[<!DOCTYPE XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">]]>
There should be nothing else in it... parse the skin package and reload. You're done.