I have this problem too, but not at every startup. It only happens
sometimes. Also gnome-tweak-tool often crashes (similar to comment #15 )
and sometimes screen locking behaves weird (see attachment) - I can take
a screenshot and it lands in my Images folder, but I can't alt-tab, or
anything like this. I have to ctrl+alt+F6, login and run

DISPLAY=:0 gnome-shell --replace

, but sometimes even this doesn't work. Some data:

Ubuntu 13.10

$ gnome-shell --version
GNOME Shell 3.8.4

$ gsettings get org.gnome.shell enabled-extensions
['alternate-...@gnome-shell-extensions.gcampax.github.com', 
'appindicatorsupp...@rgcjonas.gmail.com', 
'Applications_Overview_Tooltip@Tornado', 'c...@patapon.info', 
'drop-down-termi...@gs-extensions.zzrough.org', 'mediapla...@patapon.info', 
'notifications-alert-on-user-m...@hackedbellini.gmail.com', 'nvidiatemp@baco', 
'skypenotificat...@chrisss404.gmail.com', 'transmission-dae...@patapon.info', 
'system-moni...@paradoxxx.zero.gmail.com', 'Windows_Overview_Tooltips@Tornado', 
'windowoverlay-ic...@sustmidown.centrum.cz', 'pressure-visuali...@mecheye.net', 
'user-th...@gnome-shell-extensions.gcampax.github.com', 
'status-area-horizontal-spac...@mathematical.coffee.gmail.com', 
'newinstancewithwheelbut...@creak.foolstep.com']

BTW Windows Overview Tooltips isn't shown on
https://extensions.gnome.org/local/ . I'll disable it and try other
workarounds mentioned here.

** Attachment added: "Weird lock screen glitch"
   
https://bugs.launchpad.net/ubuntu/+source/gnome-shell/+bug/1236749/+attachment/3923306/+files/Zrzut%20ekranu%20z%202013-11-28%2017%3A11%3A35.jpg

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https://bugs.launchpad.net/bugs/1236749

Title:
  Gnome shell extensions disabled at every startup

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