There is a patch for the latest version of trillian that I know fixes Yahoo! messenger issues. You may want to head to trillian's forums to ask a question (or just find someone else who has had the same problem fixed already).
I am running Trillian Pro as we speak and I have a MSN connection. Actually I am connected to MSN, AOL, Yahoo, and ICQ and they are all on and working. Trying right-clicking the tray icon, select Connection, then Global Disconnect, then after it disconnects everything go back and reconnect.