This is so irritating issue. I had it since 10.10. I thought it's related to my Awesome WM setup, but now I see that more people have it and must be some race condition.
What I have noticed is that during booting/logging in time there's still gnome-setting-manager process belonging to gdm user. This one probably collides with newly started session and once it finishes, the theme goes gray. So I force gdm to kill it while still being gdb user:
So far the problem does not reappear, while previously I had it at every login.
[mutex:~]% cat /etc/gdm/PostLogin/Default
# Note: this is a sample and will not be run as is. Change the name of this
# file to <gdmconfdir>/PostLogin/Default for this script to be run. This
# script will be run before any setup is run on behalf of the user and is
# useful if you for example need to do some setup to create a home directory
# for the user or something like that. $HOME, $LOGIN and such will all be
# set appropriately and this script is run as root.
killall gnome-settings-daemon 1>>/tmp/log.1 2>>/tmp/log.2
killall -9 gnome-settings-daemon 1>>/tmp/log.1 2>>/tmp/log.2
[mutex:~]% ls -al !$
ls -al /etc/gdm/PostLogin/Default
-rwxr-xr-x 1 root root 561 2011-05-11 13:57 /etc/gdm/PostLogin/Default