I haven't had to fix this specific problem. But, couple things, 1) bConfiguration -> Transaction Detection -> JMS says it will auto-detect for all "incoming" JMS messages. So try and find incoming JMS messages as BT first and 2) I would add the com.ibm... JMS sub-package under Configuration -> Call Graph Settings -> Specific sub-packages / classes from the Excluded Packages to be included in call graphs and see if this helps. com.ibm* is excluded by default.
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