Let me see if I can help.
When you say 'not showing up in PCA" are you talking about the setup section or the status section? Do they show on on consoles, touch screens, or the iPhone/Android apps?
General info: In the Omni generally named = used. It's pretty simple. On my test system right next to me I have several thermostats defined in the setup. One for each type of thermostat and PESM we support. They are all named, in the name field, not just the description field. There are only two thermostats physically connected to the system. When I connect to the controller and go to status, all thermostats show up, even those the do not physically exist. The only ones that have valid readings are the ones that physically exist, the others have all 0's. So even if a thermostat dies, it should still show up, just with all 0's. If you have 2 thermostats with the same address they will both show up, but one will display all 0's and the other will have erratic values. (Because when the controller polls the thermostats "thermostat 1 give me you readings" they both respond and may/usually talk over each other.)
So check to be sure that everything is configured and named. Verify that the thermostats are addressed correctly. Finally make sure the configuration has been written to the controller.
After doing this let me know that happens.