My furnace is 6 years old. I have 3 zones with a Honeywell zone controller. I replaced the ignition module and noticed and replaced a cracked gas exhaust tube - the tube that leads to the condensate trap. The furnace will work fine once I cycle the power. However in the morning (after all programmable thermostats go into a low temperature night mode)the furnace will not run even though the thermostats are asking for heat. I don't get faults from the zone controller. Does this have anything to do with the trap being low on fluid? Please help.

In the morning when the unit is supposed to be calling for heat is power being supplied to the ignition modual? If not trace back and see what control is defective.

Are the thermostats calling for heat in the morning IE supplying a heat activating circuit to the controller and then are the controllers sending a signal to the furnace? These items need to be checked to see where the failure is.