Sorry for a tardy reply - but I just saw your post - likely it was caused by a MIDI routing issue: If you go to DEVICES > DEVICE SETUP > MIDI > MIDI PORT SETUP > look at your “In ‘All MIDI INPUTs’” column, make sure you do not have Port 2 (the REMOTE port) marked as one of you INPUTS here. Only MIDI devices you use as your controller should be marked - only devices that generate data you wish to record to MIDI Tracks. If you have the REMOTE Port marked this will cause the strange behavior, as you have described, when you activate the DAW REMOTE mode. REMOTE CONTROL Messages should be isolated on their own discreet port in their own separate Device Folder.
If you mark Port 2 as available under ALL MIDI INPUTS, when you press buttons you may hear MIDI note-ons, touching buttons or keys may open Cubase windows, etc (ghosts will seem to occupy your machine). The REMOTE port is set in the DEVICES > DEVICE SETUP > REMOTE DEVICES folder. This will keep your remote messages separated from your musical performance data which is isolated on Port 1.