Hmm. I can't explain that. Could you give more information on what you are actually seeing?
To answer your other question: when you define a MDB, the connection used to consume messages is defined using an "activation spec", not a connection factory. The activation spec is defined in ejb-jar.xml or in annotation in your MDB.
Connection factories are normally only used for outbound connections.
Unfortunately, setting imqConsumerFlowLimit (or any arbitrary property) on an activation spec or connection factory won't be possible until MQ 4.4 (which will come with Glassfish 2.1.1 when it is released later this year). I plan to write a blog posting about this soon.
Nigel
(This answer relates to the JMSRA resource adapter shipped with Glassfish and used by default to connect to MQ)
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