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The %3C and %3E are URL-encoded "<" and ">", which are already in the URL. So, I'm not sure how those would get in there multiple times. If you use Edit Link from the context menu and remove the %3C and %3E does it work?

Could you also try selecting the message in Mail and pressing shift-command-H to toggle on full header display and copy the Message-Id header? For example, one of mine looks like:

Message-Id: <>
CTO, The Omni Group