What MIDI Instruments are you using? Do they all sound out with the click or some? I have observed this phenomena using Kontakt 6.3.1 as a Rack Instrument or VSTi. Exclusively with their Factory Library drumkits (this would include kits from the old Kontakt 2 & 3 libraries as well). Seems to be the only time I ever run into this. You can clearly hear the kits behind the click.