BUG: Shopping cart and pricing are messed up sitewide

There is a problem with the pricing on the site vs pricing in the variations.

My guess (without deconstructing my clients site) is that the client put in a price, and then later added variation pricing. However this variation pricing isn't overriding the previously entered price.

Variation pricing once entered should override any previously entered pricing.

Please fix bug asap... MAJOR bug.