From my understanding of the code:
A Spigot entity optimization (Activation Range) and a vanilla optimization of ItemEntities (moving itself only three times out of four ticks) collide in such a way where ItemEntity move function is never called for some ItemEntities.
Relevant code (I hope): Link (Left: ItemEntity.class#tick, Right: ActivationRage.class)
Bug can be tested with this setup (superflat & no mobs spawning just in case): Link
Upon dropping out items and opening the trapdoors one of the four items will be bugged and will not fall on the server side, they only fall visually on client. When the trapdoors are closed the bugged item will 'return' (again just visually on the client) to its real position.
This can be fixed by changing the entity-activation-range for misc to 0. This however will cause more lag as the optimization will not work for any 'misc' type entities.
I propose either an additional entity-activation-range just for items or a boolean setting to fix this (at the cost of small performance loss)
Removing the vanilla optimization would be a mistake in my opinion as it could break some cool vanilla redstone contraptions. (Totally not the reason why I spent six hours hunting this bug)