My sister has a Tempstar 80+ furnace (model NUH 5100BFB1) with humidifier in her condo. It appears original and the condo was built in 1993. The furnace when hooked up to a simple thermostat (mercury and bi metal strip type) works fine. Turns on, heats the home, shuts down as expected. To help her out I bought a Honeywell 3200A programmable thermostat, connected the two wires, too simple. The furnace will turn on when heat is called for, then when heat is no longer needed the flame goes out, but then the fan which should only run for a short time starts to fluctuate between two speeds. It sounds like the normal fan speed then slower for just a second or two then faster for a second or two, up and down. I only left it this way for four or five minutes before turning off furnace. Hook up the old thermostat and the furnace seems to function fine. I then hooked up the new Honeywell thermostat to my furnace and it is working fine. I took my slightly older Honeywell thermostat model 3200 and hooked it up to her furnace. Again I hooked up the two wires and her furnace seemed to function properly. After 1 week she came home and turned up the heat and when the furnace went to shut down after heating the home, the fan started fluctuating between the two speeds again. She called me and I had her re-install the original thermostat and the furnace again is cycling on and off properly. I called Honeywell and they said it must be the furnace, but the furnace works with the old original simple thermostat. I do not understand and can not find any info online regarding this particular Tempstar furnace.
Any suggestions as to what might be causing the furnace fan to fluctuate this way?

Read the instructions carefully,, one step at a time in the programing part,, sounds like it not set right