Description of the issue:

You can duplicate items by dropping the tool box at the exact moment you open the GUI of the tool box. You can then take your items out of the tool box, close the GUI, pickup the tool box and the tool box will contain all of the items you just removed from the GUI, the items removed are NOT phantom items.
It's extremely difficult to do but possible. managed to replicate twice before attempting to record which resulted in utter failure.

Same type of dupe can be found in this thread OpenMods/OpenBlocks#765 (comment)

Versions & Modlist

forge-14.23.4.2756
ImmersiveEngineering-0.12-84
jei_1.12.2-4.12.0.215

I'm a bit confused right now: are you sure you are using IE build 84 (just making sure, someone got this wrong a few days ago)? We had a report of this recently (~2 months ago) and I'm pretty sure the fix I put in should work.
I wasn't able to replicate the "opening and throwing away at once", but I tested by temporarily removing the protection from the slot containing the toolbox: The GUI should close as soon as the item you're holding isn't the toolbox any more.

100% sure that it's build 84 , I originally found it in a mod pack and was able to do it alot. Decided to test in a separate instance that contained ONLY the mentioned mods above and was able to do it twice. It's extremely hard to do. The culprit could be a mix of mod interaction and server lag maybe.
The modlist that the bug was originally found is listed below.
modlist https://pastebin.com/ShX9PYCB