So, I installed an application that runs in the menu bar in OS X Mavericks. When I open that application's window (from the menu bar), there seems to be no obvious or intuitive way to switch back to that window with the keyboard after I've moved focus away from it.
When I try Cmd + Tab, I see the list of running apps (Finder, Chrome). I thought that this window was possibly associated with Finder. However, when I switch to Finder (using Cmd + Tab) and then try to use Cmd + Backtick, the window never receives focus.
I don't think it matters what the application is; I'm betting that this problem would occur with any app that runs in the menu bar and opens a new window. I will confirm this as I continue to install apps. However if you think it matters, the app in this case is called "Spectacle" from spectacleapp.com.
The same exact issue happens when you open a window like "App Store Help" from the AppStore. The OS basically leaves a window that is orphaned from the Cmd + Tab list or any other keyboard centric way of setting focus.