I'm going to go subscribe to the Samba lists and submit this as a bug/feature request. As far as I can tell, Samba has no way of using a certain WINS server for a specific interface, and part of the problem I had is due to this option missing, and it sending the wrong IP out.
I personally think that WINS is a bug. If you look at how dependant corporate networks are to WINS, it's a miracle there hasn't been a virus that overflows the WINS database. not to think about names spoofing...
The dynamic DNS with secure updates approach of win2000 and XP looks a lot more robust, though I'm not convinced yet. We're implementing it right now, so the future will tell...