In case anyone else has this issue:
We have had the issue where the 'advanced' list of role permissions disappeared off the edit 'define role page' for each of our roles.
With quite a bit of work from our support team we have discovered that this was caused by the Grade Export Checklist Plug-in. Once we removed this the permissions table reappeared.
Hoping this happens to no-one else but if it does, this was the solution for us.