In the Social configuration area of JFBConnect, there are tabs for K2 - Comments where you can enable the comments to display.
As for the K2 comments not working, I really don't know what would be causing that. When the JFBCSystem plugin is disabled, almost all functionality of JFBConnect is disabled. We shouldn't be conflicting with K2 comments anyways (we just add FB comments), so I really don't think it's caused by JFBConnect.. but I've been proven wrong before
I hope the above helps, but if you need more assistance or have any other feedback or clues as to what's going on, just let us know.
Thanks,
Alex