What soundcard are you using? Are you using ASIO drivers? Is the soundcard sync set to internal and external?
This usually happens when your project sample rate is set to something different than what the sound card is set to/capable of. If your soundcard's sync is set to external, then it will not switch to the correct resolution of the project when you open Cubase. Also I sometimes get this when for whatever reason my soundcard decides to get stubborn and doesn't switch to the proper sample rate (this usually happens if I had some other software open before opening Cubase and it doesn't properly release control over the soundcard). Most of the time you can quit Cubase, set the correct resolution on your soundcard manually using it's control panel and then launch Cubase again. Sometimes you may need to restart the computer.
Hope this helps. Good luck!
