By default, message and service instance tracking times out if a query runs longer than 60 seconds. However, the actual behavior is that the tracking times out after about 30 seconds. Additionally, the Tracking QueryTimeout registry value can’t be changed.
Cumulative update information
This problem was fixed in the following cumulative updates for BizTalk Server:
Microsoft has confirmed that this is a problem in the Microsoft products that are listed in the "Applies to" section.
For information about the service packs and cumulative update list for BizTalk Server, see KB 2555976: Service pack and cumulative update list for BizTalk Server.
For more information about BizTalk Server hotfixes, see KB 2003907: Information about BizTalk hotfixes and cumulative update support.