Well, I found this thread, but it was unhelpful as it does not address the issue.
http://vba-m.com/forum/Thread-player-2-disconnected
The issue is that when the rom is loaded, it will endlessly output the error message "LINK: Player 2 disconnected|OK" and a new one will open when you click ok.
I am not trying to do linked play, just play the game. I feel like changing the timeout in link settings might help, but I have no idea what to try, I tried 0 and 50000 with no success.
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edit:
I am running it through wine 1.3 on Ubuntu 11.10