Hi,
did you set property shoppingCart.ShoppingCartShippingOptionID in your custom web part?
The shipping option configured by code above is used by method:
/// <summary>
/// Calculates shipping cost for the given shopping cart. Shipping free limit is applied. Shipping taxes are not included. Result is in site main currency.
/// </summary>
/// <param name="cartObj">Shopping cart object</param>
protected virtual double CalculateShippingInternal(ShoppingCartInfo cartObj)
which you can override. Its result is used in method:
/// <summary>
/// Calculates total shipping for the given shopping cart. Shipping taxes are included. Result is site main currency.
/// </summary>
/// <param name="cartObj">Shopping cart object</param>
protected virtual double CalculateTotalShippingInternal(ShoppingCartInfo cartObj)
which only adds shipping tax to shipping price. The result of above methods is available in property shoppingCart.TotalShippingInMainCurrency or shoppingCart.TotalShipping (price in shopping cart currency).
If it does not help, could you please share the code of you web part and overrided method?