14.04 - Still booting from old kernel after upgrade

I upgraded 2 almost identical servers from 14.04.2 to 16.04.3 via do-release-upgrade.
One went fine but the other still boots from the old kernel. I tried all suggestions mentioned in similar situations, doing the kernel upgrade again, updating grub etc. but no luck. On the problem server I noticed there is another boot directory inside the /boot which has another grub.cfg and the old kernel and grub is coming from there.

Anyone seen this before? /etc/default/grub points to the normal /boot/grub/grub.cfg which is the new kernel but somehow thats not getting picked up.

Thanks