I have 2 websites in my Magento, each website has it store view with an specific language, currency, etc. All products are in both websites but with different prices (I changed the scope and defined each product price for each website).
One of my products (let's say product X) is a configurable product which has products A, B and C as options (these last 3 are simple products). Product X price is $50 but if I choose option C, I have a discount of $10.
So, inside Product X, in the tab Associated Products, I have products A, B and C, having C with -10 in the price field.
Everything was working fine before, but after adding a new website and setting these products to show in both stores, this discount seems to be duplicated. When I go to the product's list page, Magento shows As low as $30 for product X, but should be $40.
Ps.: I tried to explain the situation as better as I could, but feel free to ask more details.