This might be a bug, but it isn't important in the scenario you describe. The /boot partition doesn't need a boot flag. Only Windows needs it's boot partition to have the boot flag.
-- No (obvious) way to set a boot flag https://launchpad.net/bugs/41012 -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs
