I determined that ubiquity, and particularly os-prober, was leaving
partitions mounted and that subsequent mounts would be mounted atop
older ones. Ubiquity's components necessarily try to access already
mounted partitions through existing mount points. When it does so it
makes no attempt to remount the partitions and usually proceeds fine.
When it accesses a problem mount point the previous mount is hidden and
ubiquity (and any other process on the system) will be fooled into
thinking it is looking at the first partition while really looking at
the last one (until the bad mounts are corrected).

Testing with just the os-prober component of ubiquity created the same
bad mounts. The bad mounts weren't always the same. I believed that
something, probably the new nautilus version, was accessing new mounts,
sometimes preventing umounts from ubiquity from running successfully.

More information:

os-prober doesn't check the status of umount commands. I also discovered
that setting the new gconf property

/apps/nautilus/preferences/media_autorun_never

to *true* allowed proper operation in every subsequent ubiquity test and
got rid of the nautilus pop ups. This did not allow os-prober to
complete properly every time but was a great help.

Logging off all gnome sessions was successful in getting mount/umount sequences 
to run on tty1. Logging on created problems with those sequences on tty1.
 
(I believe that something other than nautilus or gnome volume manager also is 
probably, very briefly, accessing new mounts).

Adding a test to os-prober's umounts to retry after a short sleep solves
the hang and incomplete list problems but doesn't address the pop-ups
and obviously slows ubiquity. Setting the above property solved all
three problems on my system in my tests, but there still seems to be
something to potentially interfere with ubiquity other than nautilus,
though much, much, less frequently. I respectfully suggest that you
consider applying patches similar to both of those below.

-- 
When hardy's ubiquity is running from a live cd it sometimes hangs, its 
migration assistant gives an incomplete list of userid candidates, and nautilus 
pops up /home/ubuntu windows
https://bugs.launchpad.net/bugs/210620
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