Is this the Atwood Comfort Control or the Dometic branded version? There are several models with the "comfort Control" label, so we need to know which specific tstat you have. A photo would be good to help get us all on the same page.
The zones are usually set with Dip switches but the zone controls on each a/c unit have to be set properly as well. Presumably the zone controls didn't change, but maybe one has a problem?
Did you try resetting the Tstat a second time? Most Comfort Controls display the zones it detects during the reset, e.g. when "Init" is displayed. Did yours show two zones then?