I am also facing the same issue, The jms message is sent but is picked up by the MDB after a while even delay for minutes in some cases.
It seems that you solved the issue, Can you please suggest as what you did to resolve the delay in pickup?
Check whether you have configured the below extended property? If not configure and try to test the connection.
watt.server.jms.connection.pingPeriod=600
Many of these parameters are set as you administer the webMethods Integration Server using the Integration Server Administrator. watt.server.jms watt.server.jms.connection.pingPeriod Specifies how often, measured in seconds, Integration Server should ping the JMS provider. The ping serves as a keep alive request sent to the JMS provider. The default is 300 seconds (5 minutes). Important! You must restart Integration Server for the new value to take effect.