2) If Check marks disappear even after you have made and saved the changes:If you have set permissions and then apply them to anything, other than the default location, (this Folder, Sub-folder & Files) Vista adds a check mark
in the Special Permissions box. You can now view the applied permissions by clicking Advanced > Edit > selecting the User / Group > Click Edit. You may have to scroll to the bottom of the Permissions list to view it.

3) You find that the check marks for some users are shaded and in the Permissions dialog box, the check boxes for those users are unavailable: Such permissions are inherited from the folder in which the file/folder is stored, and not set explicitly. To break the inheritance chain, you have to, in the Security Tab, click 'Advanced' in the 'Advanced Security Settings' box, then click Edit and finally clear 'Include Inheritable Permissions From Objects Parent'.

4) If the Permission settings are not available: You need to check your user account rights. Are you logged in as a member of the Administrators group? Or are you the owner of the object, to set its permissions? If you are logged in as a Standard user, you will be able to view only your own permission settings. If you select another user / group on the Security tab, the permissions box would be unavailable.