If you have read any of your bookmarks and they don't clear all you have to do is 2 things.

1. Go to the series that you want to read and click on the top manga and they wait for a few minutes. This should take care of the issues you're having.
2. Click on the manga and click on remove manga from the bookmark page once it's gone click on refresh and add the manga back in from the open manga. (If you're site opens up to another window of the manga only then do this step.)

These 2 steps are what I do when I'm having the same problem as you of course I don't know if you're browser opens a new window to read the manga or not but this is how mine works and it's no problem for me.

Very2 Far

Literally skinny version of Nikado Avocado