You have several receive locations that use the MQSeries adapter in BizTalk Server. When there are many messages on a queue that must be read in order, the other MQSeries receive locations on the same BizTalk host instance stop receiving until all messages from the in-order receive location have been read.
Cumulative update information
This problem was fixed in the following cumulative updates for BizTalk Server:
Article ID: 3202740 - Last Review: 26 Jan 2017 - Revision: 3
BizTalk Server 2013 R2 Branch, BizTalk Server 2013 R2 Developer, BizTalk Server 2013 R2 Enterprise, BizTalk Server 2013 R2 Standard, BizTalk Server 2016 Branch, BizTalk Server 2016 Developer, BizTalk Server 2016 Enterprise, BizTalk Server 2016 Standard