I am currently running Ubuntu 14.04 LTS with GNOME 3.12 and encounter a problem with the Tweak Tool. Whenever I restart my machine all extension settings are getting set back do default, which is pretty annoying. I have no idea where this behaviour is coming from. Any thoughts?
While this seems to be a known bug (https://bugs.launchpad.net/ubuntu/+source/gnome-shell/+bug/1236749), I found this workaround (as stated in comment #12 on the report) :
Not sure if it works for everybody, but it works for my setup.
to elaborate
I hope this will help in resolving this issue - at lease for some. There are three possible login entries in the session menu accessible via cog to the left of the login button. Set option to "system default" instead of "gnome or classic" , extensions should now stay enabled after reboot.