We have done that and I'm not able to see what's wrong. At this point I would really like to find the specific problem and fix it instead of gutting the site and starting over again. I have a feeling that will cause even more problems than what I have now.
I've attached the most recent version of the site, is there any way you could please look at it and see what's wrong?
The live site is product.php and you can see what I'm talking about (if you need to) there by adding a product to the cart with Medium or Large option. You'll see that the price does not increase over the base price. Everything else seems to be working fine.