Eric's BizTalk 2004/2006/2009 blog

Perhaps you are restarting a host instance, maybe you are deploying, whatever, it takes forever. The problem is really that there is a spike in CPU usage.

The hot fix can be downloaded here:

http://support.microsoft.com/kb/943165

FIX: A CPU usage spike occurs on all the BizTalk hosts after you install security bulletin MS07-040 on a server that is running Microsoft BizTalk Server 2006 or Microsoft BizTalk Server 2006 R2

Don’t ever set port authentication if you are doing AS2, for your love that is all holy.

Event Type:    Error
Event Source:    BizTalk Server 2006
Event Category:    BizTalk Server 2006
Event ID:    5719
Date:        6/13/2009
Time:        12:54:19 AM
User:        N/A
Computer:   
Description:
There was a failure executing the receive pipeline: "Microsoft.BizTalk.EdiInt.DefaultPipelines.AS2EdiReceive, Microsoft.BizTalk.Edi.EdiIntPipelines, Version=3.0.1.0, Culture=neutral, PublicKeyToken=31bf3856ad364e35" Source: "Pipeline " Receive Port: "AS2Receive" URI: "/BTSHTTPReceive.dll" Reason: The party corresponding to the inbound message cannot be identified.

For more information, see Help and Support Center at http://go.microsoft.com/fwlink/events.asp.

The fix is to set the receive port to No Authentication

You need to create a 32 bit host and its subsequent host instance, otherwise you will get the following error.

Event Type:    Error
Event Source:    BizTalk Server 2006
Event Category:    BizTalk Server 2006
Event ID:    5754
Date:        6/12/2009
Time:        7:37:50 PM
User:        N/A
Computer:    HAL64
Description:
A message sent to adapter "HTTP" on send port "SendPort4" with URI http://server/BTSHTTPReceive.dll is suspended.
Error details: There was a failure executing the send pipeline: "Microsoft.BizTalk.EdiInt.DefaultPipelines.AS2Send, Microsoft.BizTalk.Edi.EdiIntPipelines, Version=3.0.1.0, Culture=neutral, PublicKeyToken=31bf3856ad364e35" Source: "Unknown " Send Port: "SendPort4" URI: http://server/BTSHTTPReceive.dll Reason: Retrieving the COM class factory for component with CLSID {254B4003-2AA7-4C82-BB2E-18BA7F22DCD2} failed due to the following error: 80040154. 
MessageId:  {9B3DB552-386E-4C46-859F-732AC39E1281}
InstanceID: {24442524-9A98-4778-A29A-93FA21AFC92B}

For more information, see Help and Support Center at http://go.microsoft.com/fwlink/events.asp.