2 ways i can suggest to overcome this.
1:i always open extra tracks just for monitoring… so lets say im recording guitar and vocal, ill create 2 tracks for the actual recording ,one for vocal and one for guitar (record button is on the monitor button is off)
then ill create 2 more tracks just for monitoring,(turn the monitor button only on them)one for the vocal and one for the guitar with the inputs you need (say input one for vocal and input 2 for guitar)
this way you always monitor and also you can adjust the levels of monitoring separately from the recorded track etc…
option 2: uninstall the MR extension and use the MR Mixer along with cubase for monitoring