There are several QFEs for BizTalk 2004 that you may want to know about, in case you encounter the situations described below.

Situation: You attempt to create or edit Receive or Send ports within the BizTalk Explorer in Visual Studio, and CPU consumption hits 100%.  Memory consumption climbs until the IDE crashes with an OutOfMemoryException.

Fix: Ask PSS for the hotfix associated with KB870619 (also known as hotfix 1185)

Situation: You have a CDATA section in an inbound xml document within an orchestration.  The CDATA section contains flat file data, with vital trailing (or leading) whitespace.  After you execute a transform in your orchestration, the CDATA designation is stripped (although the flat data is still there) - and the leading/trailing whitespace is now lost.  Curiously, using the "Test Map" feature (by right-clicking on a map in the solution explorer) doesn't exhibit this behavior.

Fix: Ask PSS for the hotfix associated with KB841563

Situation: You have a scope shape, and scope timeouts aren't working as expected.  Specifically, for blocking calls in an expression shape within the scope (like a DCOM call, etc.) where the timeout is being exceeded, you see 100% CPU consumption in the BizTalk service and the orchestration never terminates.

Fix: Ask PSS for the hotfix associated with KB811250.  (Note: this problem may have been addressed in the fix rollup released in April - I'm not sure what the ordering was here.)