I've noticed quite a few "Jomon is cheating" messages in a SP game that I started after the patch, playing as Jomon with no mods enabled (though I do have some installed) on Urraparand map. I haven't noticed any pattern to the notices yet, though that could just be me not paying attention.
But in this case I can with certainty say it's not caused by the save being old since like I said, the game was started after I'd applied the patch. The only reason I started the game was to check out the new Jomon goodies anyway.
Dunno if this helps any but thought I'd mention it.