We had some strange behaviour with BizTalk (2004 Sp1 on Windows 2003 Sp1).
Basically a receive location using a polling adapter (MQ, SQL) would stop receiving messages e.g. messages start building up in the queue, table. No event log messages are generated and BizTalk looks like it's behaving correctly, the only way to resolve it was to recycle the host instance ;0). We found nothing on the web about this specific issue from M$ in terms of a BizTalk patch. However several other people have experienced this behaviour (see links below).
We tracked it down to a bug in the system timers class in .Net 1.1. There is a patch that you need to order from MicroSoft to fix the bug. We applied the patch and everything works fine (so far).
http://www.topxml.com/Biztalk-Adapters/rn-208787_SQL-Adapter-stops-polling.aspx
http://support.microsoft.com/?kbid=900822
Roll on a swift adoption of BizTalk 2006
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