I am having trouble getting a NS2 to recognize time zones for relay 3?

SOURCE: Honeywell electronic thermostat malfunction for oil heat zone

Try changing the batteries.

SOURCE: Honeywell T87f 3855 Doesn't Activate Heater

thats becaue you need more than this zone working like you said about the master/slave this zone is a slave.

SOURCE: Honeywell 8000 Thermostat relay switch clicking noise.

It's an expensive solution but doable. Look for Honeywell's VisionPro IAQ thermostat. It works much differently than a conventional thermostat and shouldn't click at all make sure it's the 3-wire version.

SOURCE: My Honeywell EMM-3 zone controller

Hi

Thanks for using FixYa. Perofrm this test--

Connect DATS Sensor to EMM-3 (optional).
a. Reconnect power to EMM-3.
b. If system is in Purge mode, press PURGE OVERRIDE on EMM3.
c. Verify SYSTEM LED is no longer flashing. This confirms proper DATS operation. (Flashing occurs in Idle and Fan modes only.)

Also see page# 9 & 10 from this link--

Honeywell EMM-3 zone controller

Please do accept the solution if the issue is resolved or else revert for further assistance.

Thanks
Rylee

SOURCE: Zone cooling not delivering adequate air to both zones simultaneo

You need to have someone evaluate the ductwork for the home. With all zones calling, there should be an even balance of airflow. And when only one zone is calling, there should not be the tornado effect you describe.

The dampers feeding each zone may be of the wrong size. It also sounds as though you are also having a problem with your bypass damper. This damper is designed to bypass excess air when only one zone is calling. It is operated typically off the airflow alone.

Have it check out. You definitely have a problem. I would recommend getting it looked at by a company other than the installing company to remove any bias judgment or diagnosis.