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.

edit:
I am running it through wine 1.3 on Ubuntu 11.10

The linktype used in this game is unsupprted

VBA-M | NGOHQ | Post Impact Productions | TNHW | XBCD 0.2.7

So does that mean that the game is unplayable then? Will getting an older version that doesn't support linking fix the issue?

yes

VBA-M | NGOHQ | Post Impact Productions | TNHW | XBCD 0.2.7