I've been wanting to get my furnace professionally inspected anyway (hard to find people at this time of year, still waiting for phone calls), but it just so happens that it started doing this not too long ago.
Basically, it runs fine, but when the thermostat calls it to turn off, and the burner shuts off, there is a squeaky rattling noise. It sounds like it's coming from the heat exchanger area and not the blower. I'm thinking there is something loose somewhere that with heat contraction, moves and the air passing by is making it shake.
I don't think the heat exchanger is cracked or anything as my CO detector probably would have picked up on that, or I'd be feeling dizzy or be talking with Jesus.
The sound does not seem to occur during normal operation of the furnace, or if I make the blower run on it's own, did it all summer and was fine. It's when the blower is running after the furnace has ran. It's also random. I only really use the furnace in the morning and maybe at my lunch, but it seems it do it after it's ran for long enough. If I turn it on, let it run for 5 minutes then turn it off, it wont do it.
Has anyone ever heard of this?