Symptoms
A send port that has a Flat File Assembler pipeline component can't process messages when you use the BizTalk Adapter for WebSphere MQ (MQSC Adapter).
Status
Microsoft has confirmed that this is a problem in the Microsoft products that are listed in the "Applies to" section.
Resolution
This issue is fixed in the following cumulative update for Host Integration Server:
Cumulative Update 5 for Host Integration Server 2016
References
Learn about the terminology that Microsoft uses to describe software updates.