With the latest Chrome versions1, when opening links with Follow Link New Tab and Follow Comments New Tab shortcuts (by default mapped to Shift+m and m, if I'm not wrong), opened links don't get marked as visited in the current / active tab with the subreddit's posts listing.
On the other side, if I open those links the "usual" way, with my mouse, they indeed get marked as visited.
(For the reference, there also was a similar problem with another extension, Surfingkeys, which was fixed by the author, and the commit in question may provide some insights if needed.)