Thanks Theodore for the explanation, and thanks Niels for updating the
package hint from e2fsprogs to ubuntu.

What I suggest is:
1. The user should get notified that a fsck is going on, and that the partition 
will not be available until the check finishes. I consider this as a bug and 
not a simple wishlist item, as a user that is not aware of this behaviour may 
think that he/she has lost data or have some other serious problem. I have no 
idea how this could be implemented, but I guess it should be possible to 
somehow pass a message through libnotify (if that is what gives the 
notifications in the gnome-panel notification tray and it's kde/xfce 
counterparts).
2. If possible, give a progress indicator that shows the progress of fsck (this 
would be a wishlist item, but one that would be even better than just giving a 
simple text notification).
3. Have the option to cancel and reschedule the disk check. I suggest this only 
because it is possible to do so during the boot-time checks in jaunty, and 
there may be users that really want this option. This is a wishlist item that I 
don't see as important, and of course if this would be implemented this option 
should only be given to members of the admin group and it should ask for the 
password.

-- 
Automatic fsck leaves partition inaccessible without any notification.
https://bugs.launchpad.net/bugs/447816
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