In the transport I have the virtual keyboard turned off.
I have two installs of Cubase 6.5.2 and exactly the same prefs set up, however in one the keyboard shortcuts do not work with the LoopBowser/MediaBay open, even in the background. They do if you select the command from menus.
Has anyone got any tips please.
Oh,
sounds like a typical preference issue to me.
First help - delete your preferences:
Mac OS X “/Users//Library/Preferences/Cubase 6”
Windows 7 “System drive \Users< your username>\AppData\Roaming\Steinberg\Cubase 6”
.
Thank you, that did the trick
you’re welcome! 
I’ve dealt with this same problem for a while now (I’m a newbie so I haven’t had much of a desire to move quickly), but nowadays it’s becoming difficult to deal with. I deleted my preferences, but the problem persists. All of my other settings defaulted successfully. Any help would be appreciated.