Shipping was charged twice for my product by the WP e-commerce plugin when shipping was set to ‘flat rate’.
I googled it and found that this problem has been recorded, but with no solution posted and the discussion closed.
Turns out it’s not a bug, it’s just a configuration issue. I incorrectly entered a base shipping charge as well as a product-specific shipping charge.
The solution is to set all charges to zero in the Settings – Store – Shipping – Shipping Modules – Flat Rate – Settings screen.
Set the shipping charges you want in the product-specific screen.
Then, of course, test thoroughly to ensure you have the charges you expect.