This can happen where a product has different attributes e.g. a t-shirt being
either green or blue. If you add them both to your cart, and get to 'Confirm
Your Order', they appear in the order, invoice, etc., but only one is passed
through to PayPal as an item.

I think its due to:
  $this->_items[$name] 
where it appears in the AddItem function of PayPalGateway.module.php

As the name of the product is the same, the first item is  being overwrittten in
the array.