What theme do you mean, a custom Steam theme or the window manager theme?
Custom steam theme, like these http://forums.steampowered.com/forums/showthread.php?t=1161035
A future Steam client beta will have a fix for this.
This should be corrected in the current Steam beta client, are you still seeing issues.
Closing as this should be fixed.
Nothing extracted yet.
I don't know too much about bug testing but I have found that the steam overlay does not use the current theme and always defaults to the normal theme. I have encountered this issue across multiple versions of Ubuntu, Fedora, and openSUSE. I have also tested multiple themes across these systems and the problem persists throughout all of them.