Sounds like I'm having a similar issue. I'm running 1.3.9f, and have installed the Stock By Attributes add on. I'm having customers reporting that after adding products to the cart, then registering, they get the "Whoops! Sorry, but you are not allowed to perform the action requested" error. Thing is, I checked includes/classes/shopping_cart.php and it hasn't been altered from the original. Confused! I'd be so grateful of any help sorting this out.