I am using BizTalk 2006R2, I have NOT used MSMQ.
But I found that there is a mqsvc.exe running in the BizTalk server, what is the usage of mqsvc.exe in BizTalk environment?
What is the function of mqsvc.exe in BizTalk
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Microsoft Message Queue Server (MSMQ) as your question indicated. BizTalk and other systems can use that to queue messages for processing asynchronously but with guaranteed delivery.
Even if BizTalk is not using it, you need to confirm that it is not being used by other systems to communicate with each other.