Sorry to hear that you are having issues with your Saffire Pro 40.
As the previous post suggests try adjusting the buffer size within Cubase. With a lower buffer size you will experience less latency but you may notice clicks, pops, or audio dropouts as you add more tracks and/or plugins to your session. Try raising the buffer size in Cubase as a possible solution.
We have an optimization guide available on our website. I suggest that you take these steps to ensure that the PC is best suited to handle audio:
Restart the PC so that these changes can take effect then test to see if you still notice the crackling.
If you need any further assistance please feel free to contact us directly.
Derrick // Focusrite Technical Support