I had noticed this too, but I thought these achievements were limited to auto matches. But maybe they are just stuck like you said. I've won like 30 Seafarers Custom matches, but "Old Salt" still says 1/5. And I made sure to colonize all four islands in a recent custom match, but no "Empire" achievement.
I did notice in the "Robbin Wood" season that I had played the Wedding car four times but the achievement stat didn't go up. That made me think that Season matches didn't count either.