I just had an almost identical experience with a fresh xubuntu install
on a dual boot set up with win98.

I had edited /etc/fstab to create a mount to a shared vfat partition
which among other things contained my Acronis True Image disc image
files in .tib format. True Image splits the image into a set of linked
files each being the  maximum size for a fat32 partition. (I did wonder
whether the problem related to the way True Image creates this linked
set rather than the file size).

The fstab line I added was :

/dev/hda5   /media/hda5   vfat   defaults,umask=000   0   2

thus setting the fsck option to check this vfat partition.

On re-booting when it got to the file system checking part of the boot-
up sequence a mismatch between the nominal size of the first .tib file
in the set and its actual size on the disc caused it to truncate the
file to 0 bytes. The boot-up sequence then hung before it could start on
anything else and I killed it.

I edited the fsck option to 0, recreated my image files and tried
booting up xubuntu. So far it hasn't eaten my .tib files again :)

-- 
fsck.vfat truncates files of 4294967295 bytes length to 0 bytes at boot-time
https://launchpad.net/bugs/62831

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