I think I have similar problem. I've created website for my company:
www.atrus.eu and at first sight everything is working fine but after adding product to cart "checkout" button is wrong. Generated URL's have double domain, for example:
www.atrus.eu/www.atrus.eu?...
The same problem is with links to added products in the cart. And the best thing: when I back to shopping (for example via category link) and click on button "your cart" (this orange button with polish word "zobacz" on top right corner) everything in cart is ok, and I can go to checkout or product details.
Deleting SITE URL in Virtuemart config panel solves the problem partialy - product images and images in admin panel not working.
I have paid JoomSEF and Virtuemart extension. Can somebody help? We should start our shop a month ago.