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I have a gas furnace. I recently replaced a bad blower motor. At that time I also cleaned out the blower housing and squirrel cage. The AC runs fine with no vibrations or any symptoms of an off balance squirrel cage.

However, when I turn on the heat, the furnace vibrates. I think it is coming from the blower, but it seems to be turning freely and again, it runs fine with the AC.

Does the blower fan spin at different speeds for hot vs cold air, and could it still be an out of balance squirrel cage? Could something else be causing the vibration? It sounds like an slightly out of balance washer on a spin cycle.

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The blower very likely does spin at different speeds when heating vs. cooling. This is not uncommon at all. In heating mode they typically are on a low speed, while in cooling or fan mode they are typically on high speed.

As such, it could certainly be the case that there is some imbalance in your blower that excites a harmonic frequency of your furnace at low speed, but when the blower is turning faster at high speed, no sympathetic vibrations are excited; hence vibrations with heat, but not with A/C.

As others have said, it may also be the case that you have an induced draft blower for your gas furnace that is causing the vibration, but these are typically much smaller blowers than the "main" blower.

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This could be a bad draft inducer motor. This is a little motor that runs for a short while whenever your thermostat calls for heat and the furnace is in its initial firing + warmup stage.

Our furnace failed this component (when it was only around 2yrs old), and the entire house would know when the furnace started running. Vibrations around the equipment itself, plus severe knocking / rubbing / creaking sounds at some of the registers nearest the furnace are generally an indicator of your inducer motor.

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The blower motor - or squirrel cage like you call it-, is not the only moving part in the furnace; there is another motor which only runs when your A/C system is blowing hot air, its purpose is to expel the combustion gases produced by the burning fuel, usually natural gas. It is commonly called 'Exhaust Fan" . This could be what is causing the vibration/noise whenever you are using the heat. This fan is often located right below or aside the duct that protrudes from the top or side of your furnace and exits thru the roof of your house

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