It sounds like your audio buffer size in cubase is too low. In cubase if you have alot of instruments going on at once, or lots of plugins you can get some strange artifacts such as crackly audio and the audio not playing all together. Change your audio buffer size higher and see if that helps you. Although while recording real instruments I suggest you use the lowest buffer you can so you will not hear a latency. Otherwise if you have virtual instruments or lots of plugins on a track and you are just playing it back, crank that buffer size as high as you can go.
In cubase go to (Devices > Device Setup and choose your audio buffer size) Some times hitting reset in device setup will get you buy in a pinch, so you don't have to power cycle your audio interface.
Let me know if this helps.
