While we hoped to give you an answer, or an immediate resolution to the problem, the situation is still being looked at. The Marked Forums Read link at the bottom of the forums seems to cause quite a stir, as we have seen issues with it before. Why this differs from the one under the "Forum Actions" drop-down on the top of every page is unusual, and may have something to do with SEO. For now, try to use the Forum Actions drop-down, but thank you for your report. It is an issue that has re-occurred rather randomly over time, and its unpredictability makes it difficult to locate the origin of the problem. It is probably a minor bug with the site theme, a script on the main page interfering, or some internal programming that improves the front page.
The temporary solution is to use the Forum Actions drop-down for Mark Forums Read.