Wait a second-if the stat says 'furnace' or 'electric' it's a stat for a AC with heat strip isn't it?
When the stat has multiple modes-furnace/fan/AC/electric-the electric option is usually for the heat strip in the A/C. Are you sure that it's a heat pump-I know it's a dumb question? If it's got a heat strip it could be unplugged in the rooftop unit. Usually the heat pump stat specifically says 'heat pump' as an option.
I agree that if it is a heat pump and the 'ambient room thermistor'(room air temp sensor) is going bad it may not run on heat but could cool and or run the furnace.
How is the unit working when it is on A/C? When on furnace does everything work correctly? The time delays on the board could be screwed up-giving it time and being patient can be critical with heat pumps switching modes too.
Another question-is the 9000 a basement unit? and is the furnace integral to it? Could you have a bad breaker? It's probably time to break out the old tester and a screwdriver! ;)
Does anyone know if the room temp sensor is in the thermostat or rooftop unit? Or are there a few of them scattered around the unit?