I'm not sure I'd say it's a bug. It's the design.

The base is for the product.

The options are for variations of the product. Singular. One Product.

Think of a T-Shirt. Charge $10 for shirt, and +$3 for print on front, and +$2 for print on back. Still only pays $10 once for the shirt, regardless whether printed on front and/or back.

It sounds like you're trying to use your attributes to order multiples of the same product.
You may have to skip having a base price, and simply set the real prices for each of your checkboxes.