I've noticed an annoying feature of Adium as a user of another Jabber client: sometimes URLs will appear non-hyperlinked.
On investigation, I discovered that Adium is actually sending XHTML messages with the URL explicitly not linked. As a result, other clients render this as-is (what's sent is exactly what you're supposed to render, i.e. if the sender said not to link it then there was a good reason) and thus the recipient can't click on the link, whereas on the Adium side it shows them as a hyperlink.
This results in a mismatch between what the sender thought they sent ("but it works here" is the famous response) and what the recipient actually sees.
Presumably Adium's auto-hyperlinking is being done at the wrong step. Rather than doing it after sending the message, it should be doing it before sending the message. This way both users will see the same thing.
What's confusing is that sometimes they do show as linked. I suppose there must be multiple ways of inserting links into a message, and one of these ways is correctly hyperlinking the URL whereas the other isn't.