I don’t think the sample rate is the issue as that would tend to be set at the interface which seems to be working OK in your case. It might be possible that your project is running at a different sample rate than the interface but I’m not familiar with Cubase.
The most likely culprit is something on the DAW channel or master bus that is active by mistake or, you are hearing two different signals at he same time causing phase alignment issues. However, the phase problem would be more likely if you were monitoring off the input and the channel at the same time. In your case it sounds like the issue is there on playback when you aren’t playing at the same time so you would need to be recording two signals simultaneously that are a little out of time with each other. It is possible but probably unlikely.