I also use EasyBCD for my dual boots. From time to time, mostly after distribution upgrades (e.g., 13.10 -> 14.04), the link from the EasyBCD-configured bootloader to grub2 is broken by an update of grub2. Every time this has happened, the fix was simply to boot into Windows and use EasyBCD (an up-to-date version of it) to remove the broken Linux entry and re-create it again. I've never had problems with that.
If things are still broken after you have fresh entries from EasyBCD, then it might mean that your grub2 installation or configuration is corrupt. To fix that, you can basically follow these debian-family instructions here, except that you need to point the grub installation to the partition (not the hard drive) where you originally put grub2 (I assume it's on your Linux partition), so, you should do $ sudo grub-install --root-directory=/mnt/ /dev/sda1
(replacing "sda1" with whatever is the correct device identifier for your Linux partition), as opposed to what the instructions say about using "sda" or similar, which has the effect of installing grub on the MBR of the hard drive, which is not what you want.
After you've reinstalled grub2, you might have to go back to Windows again to recreate the Linux entry with EasyBCD.