I've seen this too, but only on anti-cheat servers. It's probably paranoid anti-cheat code ruining the game experience yet again. You can get back the vanished item stack back from that thieving server by opening a crafting table, btw.
Some hacked clients have a "steal all" button for swift snatching of valuables from others' chests. I guess this behavior is supposed to foil that, but it really seems overkill to me. And the problem is in chests being emptied, not in how quickly the attacker can do it. Just makes things hard for the players, while griefers continue to gank your diamonds and blow up your base.
Seriously, most servers have this "faction" or "towny" mod which encourages players to gang up on each other because if you kill someone enough you are allowed by the server to destroy their house and steal their stuff. It's to evoke a sense of epic tension between factions I guess. But the admins actively encourage that terrible grief, yet won't even let you sort your inventory claiming it's griefing. What a situation!