HVAC Heat only comes on when Fan is set to "ON" (not Auto)
The zone board's gone bad

Since upstairs is broken, yet downstairs is fine, and it's not a thermostat issue, I'd point the finger at the zone board having something wrong with it. Just to make sure, try pulling the upstairs thermostat and jumpering R to W on its base; if the heat doesn't come on, then something's dead with the W input for that zone.