the operationProperties "selectedOperation" element is not selecting the correct operation when specified in a .composite file. For example:
<operationProperties name="subtract" selectedOperation="proxyOpName" />
Following the rules of operation selection, the operation selector determined the operation should be "proxyOpName", but even though the opertionProperties element was specified to have subtract be invoked, the code actually invoked proxyOpName.
Debugged revealed the code was recognizing that a native operation should be updated, but it was retrieving the wrong information. JMSBinding.nativeOperationNames map is essentially "backwards" from what we actually want to retrieve (it was retrieving the native operation rather than the opName). So I've created a patch which create a new table mapping native operation -> opName, and updated the code as appropriate.