The logistical transporter pipes do not work correctly with vanilla chests (and possibly other storages). Items are being overwritten when they should be added to the chest.

How to reproduce:

1. Place a chest with a basic logic transporter on top, with a chest on top of that.
2. Put a stack items in the top chest
3. Change the upper part of the pipe to PULL with a configurator
4. Watch the bottom chest.

It's not only the Logistical transporter, it's also any factory block with autosort on. Every block which is moved to another slot gets deleted.
--Edit--
Fixed the issue of this comment in #4305 as it was a missed null conversion in ItemStackUtils.

@aidancbrady the original issue (first post of this) isn't solved in the latest version.