Gas and Oil Home Heating Furnaces - Thermostat question

I used to have a gold round honeywell thermostat with the mercury switch inside. It also had the backplate with the fan control/heat-cool switches on it. I was able to turn just the fan on any time I wanted to by switching the fan control to on from auto. So, fast forward 10 years or so and the thermostat has been moved (house addition), furnace been replaced, and the thermostat was replaced with a honeywell ct3200 programable unit. This system has worked fine for years, but I did notice that somewhere along the lines I lost the function of turning on the fan by itself. Since I will be installing a humidifier soon I wanted this feature back. So I checked the wiring at the tstat to find that the green wire is not connected, just the red and white. I find the place where the wire was spliced when the addition was added and sure enough the green wire was not spliced together. I check the control board in the furnace and sure enough the green wire is just hanging out in there unconnected. So I connect it all up and voila, I have this function back and the heat seems to be working fine as well. But now I notice that the fan cycles and burner cycles seem to be different than before and I could swear that the air coming out of the registers is hotter at times than it used to be. Is this because the t-stat is now controlling the fan cycles as well as the burner cycles where it all used to be just controlled by the furnace? Did I do more than just get my manual fan control back by connecting that wire? Sorry for the long post.

Is this because the t-stat is now controlling the fan cycles as well as the burner cycles
You said you had a R and a W wire to the tstat. I take it then you dont have AC on this furnace. So if you put the G wire from the tstat to the furnace. The tstat has not a thing to do with the fan . The tstat will control the burner in the furnace and the furnace will control the fan. Now with the G wire on the tstat if you turn the tstat to fan on then the fan should come on at the speed you set it at and you will have to turn the fan off at the tstat.

Great, this is exactly what I thought would happen. It just seemed like it was acting kinda funny when I was down in the basement. I thought maybe the programable thermostat had the ability to control the fan cycles through the green wire. It was probably just acting strange because I had it turned off for so long while I was working with the wires.

Your thermostat has a fuel selector switch on the back. If it is set to E it will cause the fan to start when the thermostat first calls for heat and to stop the fan when the thermostat is satisfied. In your particular case if the switch is set to E then the fan will start when the furnace goes into its trial for ignition and will blow cold air. After the furnace warms up the furnace control will "take over" and cause the fan to run for a period of time after the burner shuts down.

The fuel selector switch needs to be set to the F position and this will disable the thermostat from controlling the fan while still allowing the fan auto-manual switch to function.

See the instructions for the Chronotherm CT3200 at:

http://customer.honeywell.com/Techlit/pdf/69-0000s/69-0653.pdf

specifically page six.

Thanks for the reply. Yes, its set to F. It does seem to be working fine now.