On a late note I'd like to confirm that yes, after playing long enough, 3.1.0 slows down for me. In my case it's mid-summer 1257, and multiple forces are expanding (the AI apparently like scattershot expansion). For reference, here's the minimap:
If you want the savegame (Hinome The Lands Of Choppin07.bwa), let me know.
EDIT: Somehow I missed the latest news (which recognized the slowdown) until just after this post. Still, the offer stands if you want to see the save game.