Hi, we also have this problem. We developed this site for a local photographer, and the shipping cost is not being added to the cart total and then not going through to PayPal. No other e-commerce plugin is installed.
Image Store on the site can be found here: http://www.anievansphotography.co.uk/image-store/
Currency is £GBP, Image Store version 3.0.9 running on WordPress 3.3.1, using Invictus theme from Themeforest.