Hi, I know this has been a while since this was asked but I was having the same issue on Ebay but I believe I have figured out why this was occurring. It has to do with how a specific seller has their accepted payment methods setup. For me I found out that the seller had their payments "managed by eBay" rather than by Paypal or another method. In doing this when you log in to paypal to pay for the item you have to use the Ebay cart interface rather than the Paypal window that would normally popup which is where you can use the scorecard rewards. So you would need to just find a different seller until it works in the checkout process.
Hope this helped with your issue, even if its a few months old.