The name of CustomWorkItemHandler should be "SwitchYard Service Task" in another case always SwitchYardServiceTaskHandler will be executed.
Workaround:
To run CustomWorkItemHandler define "workItemHandler"(in switchyard.xml) as following:
<bpm:workItemHandlers>
<bpm:workItemHandler class="com.myfirm.switchyard.bpm.CustomWorkItemHandler" name="SwitchYard Service Task"/>
</bpm:workItemHandlers>
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