Permissions not saved correctly

If a module has more than one permissions, the last permission listed for that module will not have its permissions turned off for all roles.

To reproduce:

1) Find a module with more than one permission
2) Check off all permissions for all roles in the permission
3) Save the permissions
4) Hide the module found in #1
5) Visit permissions page
6) Save permissions
7) Unhide the module
8) Visit the permission page and notice the last permission will have all permission checked off for all roles