When the XMLReceive pipeline has the AllowUnrecognizedMessage property set to True, it does not track Business Activity Monitoring (BAM) activity for receive-side events in Microsoft BizTalk Server. This issue occurs when the incoming message is unrecognized. This issue also occurs when a custom pipeline that has at least one pipeline component is used on the receive side and when BAM activity is configured on receive port.
Cumulative update information
The fix that resolves this issue is included in Cumulative Update 2 for BizTalk Server 2013 R2.
Microsoft has confirmed that this is a problem in the Microsoft products that are listed in the "Applies to" section.