I just remember when I installed AC that it required me to update my .net compact framework to 3.5. There are a few forums out there that seem to support this.
Code
http://www.xperiax1.net/forum/xperia-x1/533-advanced-config-3-2-a.html
Code
http://www.careace.net/2009/03/25/the-ultimate-tweak-tool-with-advanced-configuration-tool/
Perhaps I misunderstood the question and that advanced config was working but themes weren't?? I just remember getting the same error when I installed advanced config telling me i didn't have the latest framework...?
Maybe the thread starter can clarify exactly what the problem is...?