As the water in the engine heats it expands and a small amount is expelled to the reservoir. As it cools it contracts and normally would suck water back in from the reservoir that was displaced initially. If you have the wrong or a faulty cap it cannot suck water back in but it still contracts thus causing the hoses to be squashed flat. If you had a blown head gasket I doubt it would hold the low pressure needed to flatten the hoses. Did you open the bleed on top of the thermostat housing and make sure there was no air in the system when refilling the radiator?
