With your system the same air for left and right sides blows over one temperature control door so both sides should get the same heat. A dual system has two temperature control doors and a separate duct systems for right and left and would give you the symptoms you are describing. The air goes through the AC core first and then through the heater core, The heater core is inline and downstream from the AC core.
The only thing I can think of would be an internal partially blocked heater core, water is not flowing through the entire core.