Might be the retrospective record.
If you are using Cubase’s ability to background record on selected tracks even when not recording from the transport, you will have a performance hit when that instrument track is selected.
Command/Ctrl * will dump out the buffered midi (see the Op Manual for more info on Retrospective Record)
You can find this setting in Preferences → Record → MIDI → Retrospective Record
Try disabling it and see if your issue persists.