I have a very similar problem, but I couldn't fix it with any of the suggested solutions. I am completely lost at this point.
I have a shared Firefox profile that is located in a NTFS partition, so that both Ubuntu and Windows 7 have access.
Everything works just fine except the "already running" problem when launching Firefox in Ubuntu. The funny thing is: once I navigate into the ntfs partition via nautilus (without even opening any folder), firefox will start.
Do you guys have any clue??