I have discover this Bug in the lateswt release of storefront Multi-store
By putting this here i hope it will help all developers before they struggle.. Anyway i hope this is only for multistore. When you create multiple Departement or categories in storefront you will see that your left menu navigation display all category and maybe department no mater the store or skinId you have it set.
The solution is to change "AllowEntityfiltering" from
bool AllowEntityFiltering = AppLogic.AppConfigBool("AllowEntityfiltering"
); to "AllowEntityFiltering"
you are smart enough to see the upper case "F" changes.
you can find this under . It is case sensitif. You will find it on this class
AspDotNetStorefrontControls/EntityControl