Ever since upgrade to XE6 there seems to be a bug in the application menus when you use styles, best explained with these screenshots:
The 2nd screenshot has the "22" item Visible set to False
Delphi XE6 is using a outdated version of the VCL Styles Utils
project to style the popup menus. This issue doesn't happen if the last version of the VCL Styles Utiles Project is used as replacement of the Embarcadero version. So as workaround you must download the VCL Styles Utils project from the repository, then add the units Vcl.Styles.Utils.Menus, Vcl.Styles.Utils.SysControls and Vcl.Styles.Utils.SysStyleHook to your project and finally comment or remove the Line (27) {$UNDEF UseVCLStyleUtilsMenu}
in the Vcl.Styles.Utils.Menus unit.