This is known upstream with Gaim. Have no idea with regards to Wine and the wine-systemtray.
At the moment, Metacity deals with this as best as it can, but is limited by the way that the individual applications demand attention. Feel free to give a more detailed bug report upstream: http://bugs.winehq.org/ -- Certain windows steal focus https://launchpad.net/bugs/54127 -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs
