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