Just a couple of thoughts, are you running the input hose to the correct i.e. lowest, point in the core? Also is it a crossflow radiator? As I understand it, you have to bleed that system to remove air from the highest point with those.
Your symptons sound like classic lack of water, I've had many old cars in my youth that had water leaks and that is what would happen, the heater would work, then not work. Low water level caused by an air lock would give exactly the same symptons.
Try removing the top hose from your heater core and bleeding through that, another trick is to run the front of the car up ramps to raise it's height relative to the heater then top up the system with the engine running. You may still need to bleed but the air lock should be less severe.
Graham.