Mine does this, and in my case it’s directly due to my old favourite 32 bit plugins which are running in VSTBridge. Cubase just stops when it tries to unload them, i.e. locks up when closing down, or when de-activating the project to activate another one. I have to kill the VSTBridge process to free up the main Cubase process. However I’m on Win7, could be entirely different on OSX…
If you think that’s what’s happening to you then remove some plugins from your system and see if it sorts it, then add them back and see if it breaks it again.
Mike.