I know this doesn’t really help, but MIDI works fine for me, so I don’t think it can be an issue with Server 2008. What sort of MIDI interface are you using?
3DMark Vantage
uTorrent
Pidgin
Microsoft Visual Studio 2008
NI Kontakt 3
Synthogy Ivory Standalone – The Challenge/Response version which is purportedly incompatible with Vista works fine.