As noted above: The small thermostat ( on the wall near the fan I assume) operates the fantastic fan, and The digital Thermostat operates the AC, The fan in the AC unit, and the furnace. These two systems are completely independent of each other.
The fantastic fan operates like this:
a) make sure that the Knob on the fan unit which opens and closes the hatch is pushed upward when the hatch is closed in-order that the electric motor which opens and closes the the hatch is engaged with the gear assembly for the hatch. The knob pulls down ( just slightly but with a small click) to allow you to open and close the hatch manually.
b) make sure that you select the fan speed with the circular knob on the fan unit by selecting speeds 1, 2,or 3 ( 0=fan off).
c) make sure the toggle switch is turned to on.
d) set the thermostat ( small one) to desired temperature.
When the temperature at the Thermostat is hotter that the set temperature the hatch opens and the fan turns on.
When the temperature at the thermostat is cooler that the set temperature the hatch closes and the fan turns off.
Keep in mind that ther is a water sensor on the top ( roof side)of the fan that will close the hatch and turn the fan off if it senses water. This is the "rain sensor" feature. Usually a little bit of rain comes in the hatch before it closes ( unless you have vent covers.
I see two possible problems that you could have:
a) Hardware: The thermostat contacts could be set incorrectly or be mis-aligned. Take off the thermostat cover by squeezing the left and right side with your figures hard and pulling straight out ( this is tough to do and sometimes you need to POP the edges with a small screwdriver).
Make sure take the contacts on the relay open and close at the current temperature at the thermostat ( i.e. is the setting slider at the current temperature when the contacts open and close). If not CAREFULLY ADJUST THE CONTACTS to the left or right as required. Be careful when adjusting and be patient.
I found one of my 3 thermostats ( I have 3 fantastic fans) had the contacts actually were hooked on the spring assembly and were not moving ( and my fan was always on once you raised the slider above zero).
2) But what I think that your problem probably is, is that you are running the Fantastic fan at the same time as the AC and / or furnace. What i do is turn on my fantastic fan with one or more windows open and the Digital thermostat turned off. ( NO AC or Furnace). This creates a nice freeze when the temp is hot and closes when the air is cool ( this is great for the night I find). I have found that running the AC at the same time as the Fanaticti fan will create small pockets of air which are either warmer than the room or colder that the room near the fantastic fan thermostat, resulting in unpredictable behaviuor of the fantasntic fan as you have described above.
If it gets really hot ( or really cold) I turn off the fantastic fans and turn on the AC or furnace as required ( and usually I am closing windows etc. at this point). The AC or furnace creates enough air movement with the windows closed to work great. Note that while the AC or furnace is on I will use the fantastic fan in the stool room for short ( or longer!) periods as an exhaust fan when it is required.
Boomer, the Better Half and our Yorkie - Ellie
2009 Chev 2500HD 6.0 L gas