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Looks like there may be a hook call missing somewhere. When a user shows up in the chat, and you click on the name to go to the profile, the uid is used such as /user/3. I have aliases to utilize the usernames and dont want to expose the uids.
On another note, perhaps a configuration option to control how clicking on the username works? Default is to take to profile page, maybe also options to (a) not link to anything or perhaps (b) open a private chat with the user.