I just upgraded to 1.5.5a from 1.5.4 and I have the exact same issues as report here. My order during checkout process is showing everything right. Shipping tax is included. But once the customer purchases using PayPal and then returned to the website the Shipping taxes are now not being shown. Plus the email confirmation also doesn't include the shipping taxes included. Therefore got customers calling as Paypal has charged them more then what the confirmation email showed. Of course Paypal is correct as everything was right during checkout, but tax on shipping missing after.

If anyone who also had this issue, what exactly did you do to fix the issue. Is the issues with the zones, shipping modules?