Towards the end of this game right as I am about to start building space stuff i.e. SS Engines etc. the game throws up a dialog about my action starting a war. I can't stop this action (btw I am not doing anything to start a war and have even had a mutual protection pact or alliance with the civ it warns about). When I click on "No, reconsider etc." it won't let me click ok. The only input it accepts is "Do it". Sorry the games is too big even zipped to attach.

You'll have to upload it onto the server.

This link explains how.
http://forums.civfanatics.com/announcement.php?s=&forumid=109

Sounds like it might be the "submarine bug". Do you have a sub set on a "goto" command?

Yes I do have a submarine moving, but it is in the open ocean. Weird! I will try not moving sub and see if this makes problem go away.

OK uploaded file. Definitely have subs on move. Even when I have interrupted them and told them to sentry enemy the bug happens. I don't see any transports around for them to bother, so I don't think that is the problem. I will try disbanding my subs to see if bug goes away.

It is probably one of your ships running over an enemy sub, that you can't see.