I noticed when I read an unread topic in any category (i.e. Tools of the Trade), once I read the 1st unread message and go back to read the remaining unread messages in that category, there are gone – even if I didn't read them yet.
I never recall that happing before.
Show unread posts since last visit.
2 unread messages in Tools of the Trade
Read 1 - go back and the other is gone.
What browser and version are you using? Might be a cookie/cache issue in your browser settings.
Try view all unread topics once you've "read" all unread topics since last visit, and see if the missing threads are there.