The behaviour of the "Mark as Shippped" tool has been a little troublesome here too, I access it through Seller Hub.
Sometimes it behaves normally, at other times the confirmation is shown but not all of the orders disappear from the Awaiting Shipment list right away as is usuual. For instance, I might select 5,6, 7 or 10 orders, mark them all as shipped, and receive confirmation only to find 1 or 2 still Awaiting Shipment. It seems the system is running slower lately, I find if I wait a short while and then refresh the page the remaining orders are then removed from Awaiting Shipment.
I haven't had any outright failures though, that's terrible.