Rick- I created this new thread for you.
Different issue=different thread
It's just good etiquette to the OP who is likely watching the thread to get an answer to their question (and probably getting email alerts as well).
I believe the answer to your question is this:
The thread watcher and the forum "yes/no" don't communicate with each other very well. We've always and forever had this "feature" (can't really call it a bug).
Here's what happens- your watched thread has a new post, and it shows up at the top of your homepage, so you click on it and read your thread. You jump back to the homepage, and the forum that your thread was in has a "yes", indicating that there is a new thread. You click on the forum name, but no threads are new. There aren't any new threads because you looked at the only new thread via your thread watcher. The forum doesnt know that you already looked at just the thread because you didn't visit the forum main page. I know that's clear as mud
It is especially apparent in slower forums- like the farming forum. Other busy forums will likely have other threads besides the one that you are watching to visit, thus there is still "new" stuff for your to see.