This issue is also related to coupons:
On the Manage Products for Coupon page, if I use the "add all" button at the top of the page, only the default product is added to the coupon. For example if the default product is size: 1, color: white then the coupon will work, however if size: 2, color: black is selected the coupon will not work.
The work around for this is to individually go through each product using the button next to the product and first click "remove from coupon" button and then click "add to coupon" button.
Please have a look into this.