Ah, I understand, thank you for the explanation. In my case, it's
mounted to /home/me/data (in fstab). So sure, this is not really a
critical path for the system, but it is for the user and at first I was
quite surprised that the folder that should contain all my data was
empty and I also couldn't mount it manually. Fortunately I remembered
the message about the check, but if I hadn't seen it, I (and I gess most
users) would have been quite helpless - especially because if I had
rebooted before the check was finished, it would have started again at
the next boot.

In general, I find it a good idea to check non-critical drives in the
background, but the user should be informed and have a possibility to
cancel the check. In the ideal case, when a drive can not be mounted
because it is currently checked there maybe should be a message (after
login for a drive in the fstab or when the user tries to mount it for
other drives) - like:

/mnt/... is being checked right now and cannot be mounted yet.
[Cancel check and mount] [Wait until it's ready]

But I suppose it's to late for something like that to be added in
Karmic...

-- 
fsck of non-fhs filesystem continues during boot
https://bugs.launchpad.net/bugs/445248
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