Electrical Issues Help Please!

[daveb]

There should be some kind of thermal sensor that commands and controls the fan besides the thermostat. Maybe there was an issue with the circuitry in the heater itself. You changed the batteries and all of a sudden the fan runs in a continuous mode. It's a red flag. If the thermostat was bypassed then it (the fan) would run only when the heater switch is turned on and most continue to run for a few minutes after it shuts down for safety reasons. If the thermal sensor is stuck closed or the heater circuit board is sending a "fan stay on" command it will continue to run. With the isolator bypassed I can see why you ended up with both batteries being drained. Sorry don't know much about those propane heaters.

BTW I found this on the internet:
RV furnace operation and this applies to most DSI type furnaces.
1. The Thermostat calls for heat, sending DC current to the furnace.
2. A Time Delay Relay is energized and passes battery DC power to the blower motor.
3. The blower motor and fans spin, pulling air from the Air Return and generating a stream
of air through the Heat Exchanger and out the Ducts. At the same time another fan pulls
air from the Combustion Air Intake into the Combustion Chamber and out the Exhaust.
4. The fan air stream causes the Sail switch to close as the blower gets near full speed.
5. Power flows to the High Limit Switch and onward to the Control Circuit Board.
6. The Control Circuit Board opens the gas valve and generates a spark at the DSI Igniter.
7. The Burner ignites, building heat in the Combustion Chamber.
8. Heat passes through the Heat Exchanger, warming the air circulating through the Ducts.
9. The Thermostat reaches the Set Temperature and opens.
10. Power is removed from the Control Board and the Burner shuts down.
11. The fan continues to run to cool the furnace, until the Time Delay Relay opens again.

Perhaps you have an issue with the time delay relay???
One thing for sure is it would be best to install a battery separator like a Blue Sea ML-ACR, & get the correct size batteries for a conversion with a heater. Don't rely on a starting battery and house battery to be tied together as a bank so the heater can run all night. I could be wrong but maybe the heater IS connected to the house battery. Chances are that if the isolator has been bypassed you just thought it was connected to the starting battery. Did you ever pull the starting battery and reinstall the house to see if the fan comes back on??? Make sure you keep the starting leads from contacting the chassis or there might be sparks flying.