Your problem is common on Linux boxes. When you kill Wine, Minilogin remains in memory using port 5999. On my Gentoo test server, I ended up adding
killall -9 MiniLogin.exe
to my stop script and it took care of the problem. Your mileage may vary on Ubuntu, but I don't see any reason why that won't get it. If you need a full stop script, let me know.
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