We had some issues with slow message processing on a BizTalk server due to throttling and I was just about to write a long blog post about this, when I stumbled upon this blog-entry :-)
This is a great post detailing which performance counters to use and how to determine if throttling occurs and what the cause (state) is.
http://blogs.msdn.com/b/biztalkcpr/archive/2009/05/27/throttling.aspx
Christian Staerk
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BizTalk Server