I believe the "hidden" permissions are just displayed elsewhere, probably due to mods.
I just looked, & I see the same thing. But looking in the DB at the permissions, the "extra" ones are mod-specific permissions, not listed on that page.
Note that I no longer use the mods in question, but, apparently the permissions were not deleted when the mods were deinstalled, so they're basically just orphans... Also, the mods blindly added permissions to admin, which was unnecessary, so I do see a # for those stray permissions for the admin, just like you.
Regarding the session errors, as noted in those threads, that appears to be a host/config issue. You should be able to diagnose a bit by looking at your session save path in phpinfo, and confirming the path is properly writable. I think you will only get those errors when you are using the file system for sessions, not the DB. Sometimes they are just put in temp folders that get cleared out regularly, which can cause periodic hiccups.