I forgot to mention that I seen Junkie XL in one of his videos saying he uses his metronome click from within Groove Agent, So im guessing he gets the metronome to audio file some other way then loads into Groove Agent which tempo syncs to project etc and just write in MIDI parts where you want the metronome ? thats what I gathered anyway.
So this suggestion might be very valid. Im no metronome expert though lol.