These last few days I have been having enormous problems with my BizTalk development environment running in a windows Server 2003 Virtual PC environment. Whenever the BizTalkServerApplication host was started CPU usage would stay at 100% consistently. Stopping all my applications and even deleting them changed nothing. No running or suspended instances were visible. For some reason the sqlservr.exe process was consuming all available CPU resources. I found a couple of links that helped me solve the problem:
Basically running the following SQL:
After installing the script according to the instructions provided by Microsoft solved my issues! I suspect that this could have to do with a problem with zombie messages that I have had.
There is also a hotfix available in case you have the wrong version installed. http://support.microsoft.com/kb/924715