Hello and welcome to Just answer.com, Super mechanic here. About your vehicle.
Yes there is a separate blower motor for the rear heat/ac. It is under the center console. You will want to check for power at the connector to it, however, there has been a service bulletin on some, for the power transistor, which may be the only problem with it.
August 18, 2003
Rear Blower Does Not Work
The rear center vents do not blow air at any climate control setting.
The power transistor for the rear blower has an open circuit.
Replace the rear power transistor.
Transistor Assembly: P/N 79330-S3V-A51
WARRANTY CLAIM INFORMATION
In warranty: The normal warranty applies.
Is the resistance more than 1M Ohms (1,000,000 ohms)?
YES - Replace the power transistor (go to REPAIR PROCEDURE).
NO - This service bulletin does not apply to the problem. Test the rear blower motor system for other possible causes (see page 21-76 in the 2001-02 MDX Service Manual, or page 21-79 in the 2003 MDX Service Manual).
That must be the motor. The only thing is the console has to come out for that. I could give you the steps for that if you like. In case you feel you can handle it.
Rear Blower Motor Replacement