I had a look and found one issue which could have been causing problems for marking topics as read, at least within boards with lots of posts.
But could find no such problems for marking boards as read. Perhaps there's just a misunderstanding in what you think that one should do. It does not alter the read by information for any topics, it purely updates the read by information for each board - just as if you had opened each board.
Ah, I thought it would mark all the threads as read too!
Perhaps a link to make it do that also... so that all threads within ALL BOARDS are set to read also?
To be honest, I don't think it's necessary and would probably just end up confusing confusion having two, very similar, options. We have the suggestions board though...