Just a heads up because I don't have quite enough info for a bug report:
Yesterday after upgrading I tried to give the the Admin role the new permissions, but this kept failing for some reason.
When I reproduced it on my local database with a debugger attached, I could see that it was trying to remove rights from a particular role.
Right.RemoveRole was throwing a SecurityException because "Rights can not be removed from the administrative role". I'm not sure why rights were being removed from the Admin role because I was only adding checkboxes. Unfortunately
I couldn't see which right was being removed, because I was debugging an optimized assembly with Reflector Pro.
I eventually managed to make the change. I think what may have had to do with it is that I gave the same permissions to another role first. Before that, I don't think they were in the be_Rights table (I'm using SQL Server). My guess is that the fact that I
added them to a non-system role temporarily added the necessary records for the operation to succeed on the system role?