I recently created an article on TechNet Wiki on the Monitor BizTalk Server Job.
The Monitor BizTalk Server job scans for issues, but does not fix them for you! It consist of two steps. First step is the execution of the [btsmon_Inconsistancies] stored-procedure. This procedure will on its turn call other procedures in the MessageBox, Management and Tracking database to collect error data (like messages without references). The second step is calling the procedure [btsmon_GenerateErrorString] in Management database, which involves a query of two tables [btsmon_Inconsistancies] and [btsmon_Issues].
You can read more here ….
You can also read a post by Randal on this job:
This job is especially good news for those of us responsible for keeping BizTalk Server running and healthy.
The general idea behind the job is to check for errors and report that those errors exist in one of the message box databases, the management or the tracking database. A zombie message is an example of an error that will be detected. For a complete list of all the issues see the BizTalk 2010 help on this topic.
Read the post Monitor BizTalk Server Job in BizTalk 2010.