I spent another half day or so on this.

I didn't really get anywhere.... but I think the evidence is that
neither the mountall.conf main script nor mountall itself actually
restart (the script doesn't echo and the 2nd set of fscks don't show the
"parse_filesystems" comments of the first, which are generated early in
mountall.c's main() even before daemonisation).  So, my best guess is
that for some reason mountall is losing its state information and then
either a timer timing out or a signal is sending it back to the main
loop in this amnesic state.  I don't know why it doesn't exit, but
suspect it may be hanging either due to problems communicating with a
serial console or perhaps on that last line call to
ply_boot_client_flush at a time when plymouth may already be dead (I
can't see where ply_boot_client would be set to NULL in mountall.c,
though I admit I haven't searched all the plymouth includes, but if this
theory is correct I can't figure out what restarts plymouth for the 2nd
set of fscks).  Other mysteries : why does it work the 2nd time around,
and why does it work when a large filesystem (my /var is 6GB) needs
checking.  I don't know.

Most concerning is that I can't find anything that seems to umount the
disks before that 2nd set of fscks kicks in.  If so, this means that the
2nd set of fscks is being run on mounted filesystems.  I gather this can
be dangerous.  I'm sure you're aware of this, but I'll point out that if
you put -M in your fsck calls that would make things safer - you'd no
longer be relying solely on your own internal book-keeping for running
fsck.  Maybe this would have downsides, I'm not sure.  It's just a
suggestion.

I could spend more time on this but I won't.  In fact I've made the
tactical decision to move to Debian stable branch Lenny as of tomorrow.
Goodbye and good luck!

-- 
mountall does everything twice
https://bugs.launchpad.net/bugs/605687
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