Can't edit permissions
I experienced this under Drupal 6.x - it is possibly a similar experience on Drupal 7.x.

The Apache error log (/var/log/httpd/error_log or similar) may show something similar to the following:

... [error] [client ... ] PHP Warning:  Unknown: Input variables exceeded 1000. 
    To increase the limit change max_input_vars in php.ini. in Unknown 
    on line 0, referer: https://.../admin/user/permissions


To resolve add the following to php.ini

max_input_vars = 2000


Reload Apache per your operating system and increase setting if pain persists.