Vanessa,
As long as there is one active agent in each touchpoint the priority shouldn't matter. The priority only shows what order the agents will be used, priority 2 will only be used if there are no priority 1, and priority 3 will only be used if there are no p1 or 2 agents.
If there are active agents in both touchpoints and you can run operators against the touchpoints then you maybe running into odd visual issue in the GUI.
Does 'Refreshing' the agents in the Agent console change the behavior?