Session variables should not be canceled out by making any adjustments. It looks like you are setting this other variable $_SESSION['eCartCheckoutForm_addshipping'] to yes to trigger the flat rate shipping.
So long as the checkout state is HI and this session variable is set to 'yes' then the shipping charge should be applied. I think the problem is how you are setting this addshipping session variable. Where do you set it and how are you setting it?