After testing this issue, this seems to be the cause:
The first time UbuntuOne is launched, it opens Firefox so a new account can be 
created. However, it takes a while for Firefox to actually be launched. During 
this delay, if Firefox is launched for any other reason (by clicking Manage 
Account for instance), then the two launches conflict with one another and only 
one starts up. It seems that UbuntuOne locks the Firefox profile early, so the 
UbuntuOne login page is displayed and the other launch produces the message.

If Firefox is already opened, then UbuntuOne just creates a new tab. If
Firefox is not open at all, it launches it without trouble.

In order for this issue to be fixed, either Firefox needs to startup
really fast (which upstream is working on, but won't be seen for a
little while yet), or UbuntuOne needs to lock the Firefox profile later
and launch Firefox right away instead of locking the profile and after a
small delay launching (which is what seems to happen, but may be wrong).

Either way, there is nothing that we can do on the Firefox side at this
point, so I'm moving this report to the ubuntuone-client package so the
UbuntuOne developers can consider whether or not there is a way to avoid
this conflict.

Thanks again for reporting this to Ubuntu, and please continue to let us
know about any other issues you encounter!

** Package changed: firefox (Ubuntu) => ubuntuone-client (Ubuntu)

-- 
firefox shows "close other session" on first startup
https://bugs.launchpad.net/bugs/569679
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