Comment 17 for bug 1128348

So you have to use proprietary binaries for your graphics.... hmmm... mine is an intel chip and I can use the open source drivers. I have rolled back to the LTS, though I am interested in seeing how Mir will work, so I will probably start testing 13.10 when Mir is implemented as default soon.
You might hang-out on an IRC channel and try to get some feedback there.

It seems some sort of config file (maybe in ~/.config) is being overwritten....

I am wondering if you did a fresh install of this, or if this is an update from 12.10.
I think something switched between the two (something like untiy moved from gconf to dconf.... can't really remember). And if you upgraded you might have some gremlins from the old config files crufting up your system. You might back up some of your config folders (if you don't know what that means, I wouldn't mind elaborating, though you seem to know your way around :) and then deleting the originals to see if that helps. Of course you may have to re set-up some things to get your desktop reconfigured the way you like.... but that helped me to get a usable desktop again.