When creating a RA JMS job, if you have multiple Agents, the connection object does not use the Agent defined within it.
Release : 11.2
Component : RA JMS
This is as designed; the Agent selection in the connection object is only to populate the list of available providers. The Agent definition in the job itself defines what Agent runs the job.
Documentation on the RA JMS Agent will be updated to better reflect that this behavior is as designed.