I've been pulling my hair out over this same problem. The multiplayer interface is, frankly, BAD. I've never been so irritated trying to start or play a multiplayer game. (For example, why doesn't the list of available Gamespy games automatically refresh when you post a game? Why do I need to enter a password for both my game and my civilization? Why not uncloak my password instead of making me enter it twice? It's not government secrets, for pete's sake, just a game. Why would you even NEED an option for "No cheating"? I could go on...)
It is not obvious at all that there is any sort of option that should determine war/peace status between live players. If there is, then it should not even be possible to put an offer on the table. The current diplomatic interface permits you to arbitrarily discusss some things, and not others, or teases you into thinking you CAN discuss them, but won'tlet you close the deal, and as a result is frustrating and confusing. (Why CAN'T I demand a certain city, even if they probably won't let me have it?) The window also has a tendency to pop up again immediately after you've just closed it, normally to say something completely redundant. The forbidden peace offer is the worst offender, though, since it puts an offer on the table, but will not permit you to accept it, which is maddening.
I think the diplomacy needs a serious overhaul.
This is a good game at its core, but I am apalled that it shipped in its current state, and even more disgusted that every game rag on the web seems to be giving it near perfect scores. It's not a near perfect game. It COULD be a near perfect game. Right now, it's a buggy POS.