The pages you linked are using a combination of E-junkie Shopping Cart buttons, E-junkie "PayPal Cart" buttons, and PayPal's own purchase buttons. That would account for the problems you described, as each of those button types would add items to completely separate shopping carts.
You must use E-junkie-provided button codes if you want us to process the order for you after checkout; however, You do NOT need to use our "PayPal Cart" buttons if you simply want to accept PayPal checkout payments. Those buttons also no longer work correctly in many ways due to recent changes at PayPal's end that we have been unable to work around, so we've removed them from our new Admin panel currently open for Beta testing.
Make sure you are only using your standard E-junkie Shopping Cart button codes to take orders for all your products; the E-junkie cart will show buyers a PayPal checkout button and provides full support for all our features. We would also recommend that you copy your E-junkie View Cart code in full directly from Seller Admin and paste at least one copy of that code into every page that has any number of E-junkie Add to Cart buttons. Your View Cart code is unique to you but the same for all your products, so it doesn't matter which product's button codes screen you copy it from. This code will add some javascript to your page that manages an overlay-style cart display "inside" your page.