AMQCLCHL.TAB contains client conn definitions, and you can define all the ones for all the queue managers against one queue manager and they will all go in that file. I am not aware this changed between 5.2 and 5.3 - did you by chance have the mqchl* env vars set globally on your 5.2 install? (I dont know if that would work, but might account for the difference).
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