Is the metronome recorded in the guitar track or are you hearing it in playback ?
It is possible while recording guitar track and monitoring metronome, the click is bleeding into the guitar track input inside your audio interface. However, I would expect the level to change at least some if you changed the metronome track fader.
Some older M-audio devices had really bad crosstalk but I thought they had improved.
If you have access to another audio interface, try that.
I think you can replace the metronome sound. Maybe try a sound with slower attack.