During install of the BizTalk agent, AIMS does the necessary settings on the IIS to facilitate for Isolated Hosts message tracing. In a few rare cases we have seen that AIMS is not tracing messages running under BizTalk Isolated Hosts. 

Please check the following setting in the Internet Information Services Manager:

  1. Click on Application Pools -> right click the app pool(s) that support the BizTalk processing -> select advanced settings -> ensure that "Load User Profile" is set to "True".
  2. Recycle the Application Pools were this setting was changed