The menu items that display are not solely dictated by the Function Access assigned to the Role but also from the value specified in the "Web Initial Form".
Out of box most of roles use the same form menu_frames_role.htmpl. If there is a specific Role who is either missing the Preferences, or if you would like to purposely removing the Preferences option from a role the "Web Initial Form" field should be reviewed. You can review this information by opening the specific Role, and going to tab 1 "Additional Information", and accessing Sub-tab 3, "Web Interface". By default the Web Initial Form should have menu_frames_role.htmpl.
This sample shows the role "Configuration Analyst" and their setting.
By default the "menu_frames_role.htmpl" cannot be customized through Web Screen Painter. If you wish to alter the form our recommendation would be to make a copy of the original form, use a different name, and put it into the site\mods\www\htmpl\default directory. The "Web Initial Form" field can then be altered to reference the new file. If you wish to revert to the original form just change "Web Initial Form" to the default value, menu_frames_role.htmpl.