I was trying to disable the global menu as per http://ubuntuhandbook.org/index.php/2013/07/disable-global-menu-on-ubuntu-13-10-saucy/#comment-8612, but while it didn't change anything, after running the autoremove command unity-tweak-tool broke. Obviously my first reaction was to re-install the removed package but it remains broken. TBH I don't know if it is even related or just a coincidence.

When I start it from the launcher it just blinks and disappear. When I start it from terminal I get this error:

$ gnome-tweak-tool 
WARNING : Shell not installed or running 
WARNING : Error detecting shell 
Traceback (most recent call last):   
  File "/usr/lib/python2.7/dist-packages/gtweak/tweaks/tweak_shell_extensions.py", line 199, in __init__
    raise Exception("Shell not running or DBus service not available") 
Exception: Shell not running or DBus service not available 
INFO    : GSettings missing key org.gnome.nautilus.desktop (key computer-icon-visible) 
WARNING : Shell not running 
None 
INFO    : GSettings missing key org.gnome.mutter (key workspaces-only-on-primary)  
Segmentation fault (core dumped)

I had a look with dconf-editor if I could just add the missing key, but apparently keys aren't meant to be added "by hand".

So how can I fix this? I'd rather prefer not having to reinstall everything.

Which package is broken, can I just reinstall that?

EDIT:

I found by being root gnome-tweak-tool no longer crashed so possibly a permission issue somewhere. I don't know that I changed any permissions.

Another related problem, actually the reason I noticed the problem at all, is that unity-tweak-tool seem no longer to want to save the values edited. I normally just have the Unity launcher on the primary display but wanted to check what it was like having it on both. I didn't like it so I went into unity-tweak-tool to set it back - but regardless how many time I tick "only primary display" it never changes anything. What does the Unity-tweak-tool actually change and can I do this directly somehow?