It seems fluxgui had crashed previously, or maybe I had killed it some days ago and forgot about it entirely. When I tried to restart it, it didn't do anything. Launching it from the command line returned the "Fix the "fluxgui is already running, exiting"" message.
Looking at the most recent version of fluxgui code, I thought there would be some sort of .pid file in my home directory:
self.pidfile = os.path.expanduser("~/.fluxgui.pid")
but I was wrong; there wasn't any fluxgui.pid file in my directory. The git version is not the same that is published in the PPA, and as such there might have been some changes to where the PID file is saved.
I found mine was actually in /tmp, so the only thing I needed doing was deleting the file:
Obviously, unless your username is sole too, the name of your file will be different, so have a look at /tmp before trying to delete anything :-P
sole@courgette:~$ ls -l /tmp/flux* -rw-r--r-- 1 sole sole 4 2011-08-01 08:21 /tmp/fluxgui_sole.pid -rw-r--r-- 1 sole sole 0 2011-08-01 08:21 /tmp/fluxlog.txt