Any user with a ~ status along with other non ~ users will on a seemingly random basis not have the status messages for their disconnects or nick changes displayed either in the main chat window or in the channel user list. EG, user ~TestPerson? will change their nick to ~Test2, but no "TestPerson? is now known as Test2" message will appear, and they will still be listed as ~TestPerson? in the user list, along with ~TestPerson? will disconnect but no "TestPerson? has disconnected" message will display, leaving them in the user list. You also can't get info through the context menu on users with the ~ flag.
I've only seen this happen on the 2d38 nightly build, and it seems that it's something to do with the fact that users with the owner ~ flag set are being mishandled.