I checked on this and it looks like it's working properly for more current customers.
The way it works is this - when we received the notification that a transaction is successful, we mark the current cart as completed. It remains invisible to the end user and a new empty cart is used.
It's possible that you messed around with the cart in the year since you originally purchased VaultWiki, or that it wasn't working properly way back at the start of that year.
Anyway, there was a bug which needed to be dealt with. We base the "current cart" on timestamps. If the timestamp of the user's cart is later than the timestamp that the transaction was sent out for approval, then the cart will not be cleared. We do this because you can still make changes to the cart (e.g. edit quantity, or add another item) while it was out for approval, and we expect that you'd rather not lose the changes you have made (even though they wouldn't apply to the pending transaction). For the bug, the timestamp was not being updated and was using the earliest time that you opened the cart since you last purchased something. This was incorrect, as mentioned above, it can lead to some users losing the contents unexpectedly.