The question Tor Browser Says Firefox is Already Running is very related to this issue but I couldn't add a comment as I am new to this site.
I have noticed ever since 3.6.4 that although the Tor connection is made and can be used by other configured software. The Tor Browser Bundle Firefox will not start up first time. I can run Thunderbird/birdie using the connection and it works fine. Looking at the process list it says that
tor.firefox is running (but it can't be seen). The only way to get it to open is to kill the process and restart.
I was hoping that there was a bug that would have gotten fixed by 3.6.5 but it wasn't. It recently takes about 5 tries to get it started eventually.
As advised in this other thread Tor Browser Bundle will run on a completely different disk and away from any system files. Even regular FF configured to use Tor will run fine on top of the tor.process.
Out of a unsubstantiated suspicion I do not use any other connection over such a process until I get Tor Browser Bundle to run properly and verify the connection is correct.
I rarely use a couple of plugins and disabling or deleting them and reinstalling the bundle had no effect on this behavior.
I don't recall this ever happening before 3.6.4 and 3.6.5 made no difference.