Yes. The BPS Pro 9.8 upgrade focused on 2 primary things: new htaccess code and the Plugin Firewall AutoPilot Mode.
Ok well if everything is working with the exclude rules then we will just call it a mystery. Since you are the only person who reported this particular issue/problem then it was just some kind of isolated thing that was occurring on your sites for whatever reason.
Yep Plugin Firewall AutoPilot Mode is a huge time saver. There are a couple of adjustments/additions that need to be made, but that is always par for the course with any new thing that is created == fine tuning for the other 1,000 scenarios you did not think of during development.