A vista or Windows 7 boot disk has a real handy feature called Startup Repair. This feature is conspicuously missing from the Server 2008 disc… or is it?

http://www.binarywar.com/2010/01/windows-server-2008-bootmgr-is-missing-error/

It is there, you just have to run it from the command prompt. And that fixed it!

x:\sources\recovery\StartRep.exe