We've had a problem with our BizTalk Servers for quite a while.  Receive ports to a particular file server would seem to shutdown almost at random.  After much searching of the internet, there was a consenus to build a port watcher application using BizTalk WMI.  We did this and it worked, ports would stop and the port watcher would kick them in the butt to get them going again.  But this was just a band-aid to a huge sore under the surface.  After almost a year of this, a re-researching of the problem finally gave way to a helpful post and then a solution! 

It turns out that when a BizTalk Server is checking LOTS of directories on the same server, the network BIOS command limit can be reached:

"This issue may occur if the client computer submits simultaneous, long-term requests against a file server that uses the Server Message Block (SMB) protocol. An example of a long-term request is when a client computer uses the FindFirstChangeNotification function to monitor a server share for changes."

"This issue may occur if the MaxCmds registry value setting on the client is less than 50, or the MaxMpxCt registry value setting on the server is less than 50."

So, per the kb article, an increase of the MaxCmds regsitry entry to 500 solves the problem (after a reboot)!  Not a BizTalk problem at all.  The limitation in the Windows 2003 OS designed to throttle its workload (for good reason) was causing the receive location to shutdown.  The error message wasn't very helpful from BizTalk as it really didn't provide a good error code or reason to point to the command limit that was eventually found to be the problem.  Now if I can only figure out why my File Recieve loactions to DFS shares do the same thing!