First of all, I'm not sure what "red dots" you are talking about. I presume it has to do with the particular style you are using and indicates posts not read since your last session. And, that is the key to understanding those notifications. Each time you log in is considered a separate session. The flags pointing out what is still unread by you are only valid for the current session. If you log off and then log back in again right away, a new session is created and the flags are gone.
I suspect you know all the above, so let me point out one other quirk of our board. The only style that is more or less guarenteed to work all the time is sub-silver. Unfortunately it is a boring style and not many people use it. All the other styles were created by third parties and may or may not be updated to work with the current version of the software. Unless there are major flaws, I keep these not so perfect styles available because people like them in spite of their shortcommings.
If you are having a consistent problem, change the style to sub-silver. If the problem goes away the style has a bug in it. Let me know about the bug so that I can try to do something about it. or confess that I'm lost as well

Inside every older person is a younger person wondering what the hell happened.