Personally I see no benefit to what you are doing GPT/EFI... My triple boot setup (Windows 7 Ult. 64-bit, Server 2008 R2, and Ubuntu 11.04 64-bit) work fine using the tried and true MBR setup... What are you experiencing??? What exactly is it doing???
Is your boot disk over 2TB? If so, it needes formatted as GPT and windows 7 can only boot from GPT drives if you have an EFI motherboard.