[MoMan]

If I read the thread then the notification disappear (as designed). Issue here is that after marking all threads as read (mark forums as read) the notifications for subscribed threads don't disappear.

You're right, that indeed seems to be the behavior for the non-memcached version. That's because, unlike I thought, the threadread table is never updated.

I see two solutions:
1. Checking the last time the forum was marked read before running the subscribed thread query
2. Updating threadread where userid = $vbulletin->userinfo['userid'] with TIMENOW when $_REQUEST['do'] == 'markread' by adding code to the plugin