You CANNOT upgrade Windows Server 2003 x64 to Windows Server 2008 x64 if Exchange Server 2007 SP1 is already on the box.
No, no, not no way not no how.
I have ranted: http://markarnold.blogspot.com/2008/02/windows-2003-to-2008-with-exchange-sp1.html
Oh, and just for kicks and giggles I took a...