Just in case this what you're trying: EasyBCD supports autoconfig for both grub and grub2; however autoconfig with manual specification of which decide to search for a grub2 installation in case multiple are installed is only supported for legacy grub.
Xubuntu 12.04 is installed as a stand alone on disk one. Grub 2 in its HDD MBR with option to start the Win 7 which is a stand alone on HDD2. I've tried NeoGrub and Grub2 from easy BCD in the Win 7 installation. It just give me a Grub carrot prompt when I boot and tell Bios to start at the Windows disk. I get the selector for Windows or Linux/grub, but when choosing the later it doesn't use what is already on the Linux disk to allow me to chose from that Grub2 and get to the linux login screen.
So BCD will not work with multiple HDD each with their own different MBRs unless they are all windows?