Right below the Stormtrack logo and above the bread crumb trail is an option to "Mark Forums Read". I apologize but that isn't a function I ever use, but was there a separate one for marking messages read as well as forums? I toggled back to STv2 and couldn't seem to find it. Please let me know.
FWIW, there's a Mark Forums Read link in the top bar that comes down, which is available on what appears to be all pages.
With that said, I dug through a bunch of the CSS code the other day and found the offending entry, but never was able to figure out how to fix it in the interface so it 'stayed' during upgrades. I'd rather not edit the files directly.