In Microsoft BizTalk Server 2010, BizTalk Server 2013 R2, or BizTalk Server 2013, you use the MQSeries adapter to receive and process a large volume of messages. However, you notice that the messages are not kept in the correct order, even though the Order Delivery option is enabled in the receive location. In this situation, no errors are logged in either the System log or the Application log on the BizTalk server.
Cumulative update information
This issue was first fixed in the following cumulative update of BizTalk Server:
Note MQSAgent.dll must be updated on the IBM WebSphere MQ server to the same Cumulative Update level as on BizTalk Server. To do this, make sure that you run the same CU setup on IBM WebSphere MQ Server. You may experience performance issues if you run mismatched versions.
Microsoft has confirmed that this is a problem in the Microsoft products that are listed in the "Applies to" section.