Resolution:
TIBCO ActiveMatrix BusinessWorks Plug-in for WebSphere MQ 7.3.0 uses s WebSphere client API for Java. The plug-in does not support “automatic client re-connection" where by if the primary queue manager goes away the client will eventually reconnect to the alternate server. JMS over MQ is described as supporting this feature which can be used to get automatic re-connection to work that way. Detailed information can be found at the Websphere MQ documentation for 7.5, Section "Configuring -> Availability, recovery and restart ->Automatic Client reconnection.
When the put activity is in a loop of a BW process, the re-connection does not work because the put is in a loop and uses a queue manager connection which is cached at the process level. If the scenario were repeated such that if a new process started each time, it would get a new connection and when the switch-over had completed the put would work. The Subscriber works this way and would have eventually reconnected. A workaround is to use a timer that starts the put process every 10 seconds.