April 29, 2012 2:14 AM PDT
Hello, the issue you are having I think is that some applications are now gtk 3 such as Update manager, Brasero etc,
The Equinox Themes are only gtk2 so any gtk 3 apps wont use it and use there default theme.
As far as I know there is no gtk 3 port for the Equinox themes yet.
To fix this for me I downloaded the Elementary 3 theme and unpacked it in to my .themes folder,
then in synaptic I installed Murrine gtk engine and the Aurora gtk engine.
Also I installed the Elementary Icon theme from Synaptic.
Once installed open up Customize Look and Feel and set the theme to Elementary and Icons Elementary, Log out and and back in and things should look allot better
The only App I have found so far that wont use the Elementary theme is Synaptic, everything else seems ok
Get the theme here: https://launchpad.net/egtk/+download
Hope this helps.