We've been having a heck of a time lately with the BizTalk working queues filling up with ghost messages.  The level of blocking in the Database had become unbearable at certain times.  We had no idea where it was coming from as our activity levels have remained relatively constant (we hadn't found out about the queues yet).  We worked with MS support to do some cleanup of our produciton environment.  This seemed to help but then the queues kept filling up again.  After some focuse digging, we managed to stear ourselves and MS support to the solution.  A new hotfix just off the presses - KB936536.  We've applied it today and will see if it works.  I will post a more complete write up in a few days.