There used to be a USB audio dropout bug in DT and DN that’s now in the M:C. It hasn’t been fixed yet, as far as I know. More info here. This might be the problem that you’re suffering from. EDIT: Ah sorry, that bug’s about USB audio going into the Cycles.
An unrelated issue: I got massive dropouts from trying to MIDI-control the Cycles via DAW while recording (a lot of MIDI data with multiple tracks etc). I got an answer from Elektron that this is simply not possible due to hardware limitations. It seems like that’s not what you’re trying to do, though, but I’ll mention it here just in case, if someone comes looking.