I’ve just read this thread over on the BizTalk newsgroups relating to a failing BizTalk 2004 custom receive pipeline following a side-by-side installation of the .Net 2.0 Framework.
I was always under the impression that BizTalk 2004 would ‘just work’ with a side-by-side install of .Net 2.0… obviously not. A fellow poster, Saravana, points us to Microsoft KB Article 841405 - it would appear that BizTalk 2004 versions prior to SP2 cannot run with .Net 2.0 installed alongside. So if you want to run both versions of the framework, upgrade to BTS04 SP2.
Given that this is news to me, I thought I would post to the community (thanks to Saravana for the pointer)!
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