Do you have it set on auto when this happens? Maybe something is wrong with the cabin temperature sensor and its telling the control unit to turn off the heat because it thinks it's too hot in the car.

When the heater turns on and off in my car (300E), it makes a clicking sound that's audible inside the car, but it doesnt come from the middle, it comes from the passenger side where the valve is located. I dont think the vacuum pods make clicking noises, rather, they make a kind of muffled "pop", but anythings possible.

Was there any air coming out of the middle vents before/after you heard this click? If there was no air coming out before or after the click, then the center vent pod is not the issue. I seriously think something is making the monovalve shut off your coolant supply to the heater core. This is just my unofficial $.02 Good luck!

__________________
Streetside: 1987 Mercedes 300E Petrol Blue/Green
2014 Ford Mustang Grabber Blue
1999 Ford Ranger Green

Dockside: 1968 Eltro 17
1985 Silverton 34C