System_advanced_misc.php and maybe other files are not updated in latest builds.
I have tried to update different versions on different machines:
30 may 2012
snapshot from 9 march.
Both version are hdd full install from iso/memstick images
Both of them showed me after update that the last changes in system_advanced_misc.php are made on march 2013 and on may 2012 version before update it was different from current version, there was no thermal sensor selection, now it is, so it is updated but with some older march/i don't know which version.
In your firmware update settings do you have the gitsync after update selection active?
The repository URL changed around then, and if you have the gitsync option active (which nobody really should at this stage), it could be updating and then the old/stale downloaded gitsync files could be getting copied over your filesystem.
Looks like this is the problem.
pfSsh.php playback gitsync master
gives me (see image)
What is new URL for gitsync master branch?
don't gitsync. Disable the gitsync option, force a firmware upgrade, and just run that way. You do not need/want gitsync on these days. That was an old method of keeping IPv6 code active on 2.0 snapshots and it is not needed now, and as you've found, can cause problems.
If you blow away the /root/pfSense/ dir it will pick up the right one automatically if you're on a current snapshot if you really must gitsync.
Thanks jimp! You are the best ;D