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I have this same problem. However, the problem doesn't occur with all emails -- just with all emails from a certain domain. i.e. for everyone at that particular company, this behavior is broken. For others it seems to work fine. I can't make out what may be the cause.

I do have MailTags installed, but I tried this using both "Mail" and "Mail with MailTags" -- selecting one or the other of the options. Behavior was the same for both.

Dragging the message itself into the note field creates a link that works in all cases, but it's an extra step.