I can only confirm, the last one of your 3 orders, the one that hasn't been refunded, has been correctly activated so, it's just not possible the Addon Manager wouldn't show as not active.
NOTE THAT, since you purchase two products together to get the discount, only the FIRST one will be activated automatically, the other one has to be activated manually using the "Register Serial" option of the Addon Manager, with the 2nd Serial Number found in your purchase receipt.
Just be careful to use the correct order, since the first two has been refunded, you can't activate their Serials anymore, so you need to use Serial found in the 3rd one.