I think this was fixed with 1.9.3 which is beta. Who knows if it will ever come out of beta status. If you click on the quick links above all the posts and instead of going back to the root of your forum, click backwards. For example your top forum is 1 and you have one subforum named 2 and one subforum under that named 3. When you read a post under 3, instead of clicking on 1 to go back to the main forum, click 3, 2, then 1 and it will mark it correctly.
No help on the counter here.