We are looking into adding the updated permissions helper in our next release, so I have been playing with it on nightly. It seems that as the OOTB instructor role, my changes to the group permissions for a tool are not saved.
Login as the OOTB instructor role
Make sure there is at least one group in your site
Go to the assignments tool (or any tool with the permissions widget)
Select that you would like to set permissions for your group
Make changes and hit "Save"
It seems as though your changes were successful, but if you go back to the permissions widget and look at the group permissions, they were not saved. I can edit the site-level permissions successfully, and I am able to edit the group permissions if I am using the admin account.
I was also able to reproduce using the "maintain" role on qa3-us.