Hey there! Note that only after the running time of the movie has passed will it be marked watched in your Trakt profile. And only then can SeriesGuide download that change the next time it syncs with your Trakt profile.
Maybe you can verify by explicitly marking a movie as watched on the Trakt website and then check if on the next sync it is marked as watched in SeriesGuide.
Yes, I tried marking as watched on Trakt and I still get the movie on SG History (under the title "a recently watched’), but it is not marked as watched when I go into the movie details page on SG.