MC 1.12.2
Forge 14.23.55.2768
realfilingcabinet-1.12.1-0.1.84
No other mods present to rule out conflicts with other mods

Put a single empty folder into a 2x2 or 3x3 crafting grid
Put a stack of items into the grid
Pick up the stack of items from the grid
All items in the stack except for one have been deleted

The ONLY item stack unaffected by this is a stack of other empty folders. Yes. I checked all vanilla item stacks.

I was not aware that this was already reported, I didn't find anything similar to my problem in the open issues. Apologies.