Gnome-Shell forgets theme after reboot?

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http://askubuntu.com – I am using Ubuntu 12.10 with Gnome-Shell from the gnome-3-team/gnome3 ppa. This is working great, and I have my custom theme setup. The only issue I am running into is that Gnome-Shell seems to forget the theme after every reboot. If I open gnome-tweak-tool the correct theme is selected, however it is not applied; if I select anything else and then re-select the theme it is then applied correctly. What could be causing this? It does not seem to be related to a specific theme, as I am getting the issue with both Mountain Shell and Elegance Colours. (HowTos)