A dumb question perhaps, but are you certain that you have the x64 edition of Win 2003, and not the one for Itanium-based systems?
And what do you mean with "trying to load win 2003 64 bit onto my [..] system"? Is it during installation of the OS, or did installation succeed and you are having troubles booting it or what?
I am running Windows XP Pro X64 with SQL Server 2005 X64 Developer Edition on my AMD 64 system with no problems.