I notice a slight increase in flow when I hit recirc.

Is the rear system putting out air any colder than the front? When you use the front head unit to change the supply zones, are they all correct? Have you cranked the temp all the way up to make sure heating is working correctly?

If the rear system is working correctly, I'd suspect the head unit. They have a self diagnostic feature, but mine was bad and didn't throw any errors. Drove me nuts for a day or two.