Progression saving issue

Here is the problem. I've read some stuff about vehicles, plants etc. in the handbook. Now I log in and see this stuff is still marked as unread. So, I had to reread it to get rid of that irritating exclamation marks. Now to the more serious problems. I also don't get why the game is not started from the moment I have pressed the save button. It seems the game starts often from the checkpoint that was before the last one.

FWIW I play via Steam.