My MOTD is showing:

*** /dev/md2 will be checked for errors at next reboot ***
*** /dev/md1 will be checked for errors at next reboot ***
*** /dev/md3 will be checked for errors at next reboot ***

However, a standard sudo shutdown -r now does not appear to check the disks and the message remains.

My guess is that the partitions 'should' be checked and that they are not being... so how can I get Ubuntu to check the partitions at reboot and keep things nice and safe?

Update - this is the output of cat /etc/fstab

proc /proc proc defaults 0 0
none /dev/pts devpts gid=5,mode=620 0 0
/dev/md/0 none swap sw 0 0
/dev/md/1 /boot ext3 defaults 0 0
/dev/md/2 / ext4 defaults 0 0
/dev/md/3 /home ext4 defaults 0 0

Update 2 - One message gone...

Using @christianwolff's suggestions...

sudo rm /var/lib/update-notifier/fsck-at-reboot 
sudo touch /forcefsck
sudo shutdown -r now

And now the motd is down to

*** /dev/md1 will be checked for errors at next reboot ***
*** /dev/md3 will be checked for errors at next reboot ***

So 'md2(ext4)' has been checked and the message updated.