I'm thinking sail switch or possibly an obstruction in the intake or ducting. What was the power source when you had the furnace out? Were you using the same wires just extended from the RV? If the power source or wiring was different it might be spinning the fan at different speeds.
If you really want to get involved with it try pulling the furnace and measure the voltage at the furnace when you power it up. Then install it and measure the voltage again right at the furnace and see if it's different/lower.
It could be that the sail switch is going bad and has some resistance to movement. When the furnace is out there is no resistance to heater intake or exhaust so the fan can spin a bit faster and lift the sail switch. When you install the furnace there is a bit more resistance to airflow which causes the sail switch to not lift quite high enough.