GRUB-2 is a pain. Easy BCD will find the grub.cfg file that is in the “boot/grub” folder In the first Linux partition that uses grub-2. See my post below about how to copy the grub.cfg file from the second installation to the first.
Booting multiple Ubuntu’s
http://neosmart.net/forums/showthread.php?t=7664&highlight=grub
Another thing you can try is to install one of the Ubuntu’s towards the back end of the hard disk first. Then install the other Ubuntu towards the front of the hard disk. Then the grub.CFG file in the first Ubuntu should have the boot loader menu for both Ubuntu’s.
The best you’re going to get out of Easy BCD is one entry for Ubuntu. Then you go into the grub-2 boot loader menu where you will have boot choices for both Ubuntu’s.
The above of course applies to the newer distributions of Ubuntu which use grub-2. Some of the older distributions use grub-1. For these distributions individual boot options can be made in Easy BCD