inputs not making sense

hi, first of all I am going to say that this (Cubase artist 8) is the most un user friendly and over complicated software I have ever used.

I am having a problem with the audio inputs. I am using a motu 16a with usb into my pc laptop. I have started a project and recorded 2 stereo tracks drums and a synth (audio using inputs 1+2 as stereo). next I wanted to record a mono track so I set one up and set audio input 3 to go to it. now the desk is sending to 3, the motu is receiving on 3 but the Cubase cant hear it. after checking all wiring many times I swapped the inputs in Cubase to various numbers (remember audio is only being sent to input 3),. so input 1 and 2 and 9 all allow the audio in. any ideas what the hell is going on?