Thanks for posting back with the cart pages. I was able to do some testing and got the shipping to be taxed by doing the following.
In the cart object open up the tax rule that you currently have in place, you just need to update the calculation portion. Instead of basing the value on the cart's subtotal you should select the taxable total for the cart, you will also need to specify to 'times' it by the session variable $_SESSION['eCartCheckoutForm_counties'] again.
When I did this the shipping and tax were working just as expected.