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.

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https://bugs.launchpad.net/bugs/1128348

Title:
  Unity starts without panels

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