So, I'm using Magmi's ingest functionality to run my own instance of Magmi to import product stocks.
I'm setting an array:
array("sku"=>$sku, "stock_id"=>$key, "qty"=>$qty)
Then ingesting that array. Inventory with positive numbers get imported just fine and updates the old number with the new number.
However, when the new number is negative, instead of setting the inventory amount to that negative number, Magmi subtracts the new inventory from the old inventory.
Example: old inventory is 5, new inventory is -3 and after ingesting the -3, the new inventory number is 2 (where it should just be set to -3).
This effect is cumulative. Ingesting the same negative multiple times keeps driving the negative inventory lower.