So the server i play on, Alphacrafters, has had this issue for the last couple weeks. When attempting to move mass amounts of items using Shift + Double-click instead of moving the items it will close the container screen and drop the stack you were holding on the ground. when you open your inv it looks like the stacks were all moved, but clicking on one will cause most of them to vanish and show only 3 stacks having been moved. opening a container will also show this.
This is a vanilla SMP server running in 1.11.2
They use Spartan anti-cheat
They use something called AlphaCore to control clans, claims, homes and TPs
I dont know what other info might be needed to diagnose the issue. The Admins and owners haven't been able to figure it out so I'm trying to get some info for them.