Quote Originally Posted by dannyboy79 View Post
you'll have to run fsck from a livecd that doesn't mount your / (root) partition. Otherwise, no matter what your / partition is always going to get mounted if you run ubuntu which is installed on your computer. You will not be able to unmount / because it's in use by the system.

Maybe someone else will come along and be able to figure out why fsck isn't running when it should be. Have you tried a search within the forum or goggle?
Another safe way to do is open terminal and do
Code:
sudo touch /forcefsck
and on the next reboot it will start the fsck checking like if it had reached 30 boots (which obviously does not work for you for some reason).

Thus, every time you want to do a fsck, give the above command and reboot.

Hope that helps you

P.S.: and yes indeed, the warning that fcsk is giving you is valid. Never do a fsck checking on a mounted partition. Only the above command is safe.