Debug Multistore magento

After updating from 1.4 to 1.7 our Magento shop has some problems: - Internet Explorer 9.0 users can go the cart page but can't go to checkout - Rewriting urls problems (when adding categories or rewriting existing urls the site crashes a lot) - One of the shops has a weird frontend with codes like .....phtml in it. All other sites are running allright. - Some products I can't duplicate - Structure of onvoice of English site is different then the dutch, german and french