Not loaded a custom map ever (ie, not knowingly. I've played various long AI campaigns but always with the Default map setting selected at the campaign generation screen).
Preferences are set to 200 x 160 and were set before the start of this battle.
I experimented with a completely new campaign and got a 200 x 160 map.
So the issue is with changing map size during a campaign, it appears to be stuck on the map size used for previous battles in this campaign. If this is how it is then fine, but it doesn't seem to be what is supposed to happen and contradicts the game guide.
If anyone else has seen the same thing as me, or has successfully changed map size during a long campaign vs AI please contribute to the post.
cheers,
Tim