Ah, that's the issue. In the old system the "mark all read" button worked even if messages were selected. In fact my recollection was that I had to "select all" messages before hitting the "mark all read" button, but that may have been a misunderstanding on my part.
Adding a note at the top to not have any messages selected when hitting the "mark all read" button would help.
I don't think the small delay matters, but I guess any note could explain that.