Building on it being an SSD/race problem, I decided to add a delay
before gnome-settings-daemon would start. The relevant file that I
changed was /etc/xdg/autostart/gnome-settings-daemon.desktop. I changed
the line:

Exec=/usr/lib/gnome-settings-daemon/gnome-settings-daemon

to this:

Exec=bash -c "sleep 2; /usr/lib/gnome-settings-daemon/gnome-settings-
daemon"

to add a 2 second delay. And after rebooting, the theme is now properly
applied. Hope this helps in finding a proper fix.

-- 
Meerkat (10.10) does not apply theme properly
https://bugs.launchpad.net/bugs/649809
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