So far, flint and bronze spears work fine for me. When a spear is put in a quickslot, the game remembers well where to replace it when it picks it up again. Only exception is when inventory is full, and another item si auto-picked up and takes that quickslot.

Did you remap middle mouse button (the one used to launch the spear)?
Did you deactivate the auto-loot mod (V key)?

What can happen also is that you actually lose a thrown spear, because of a decline, or some misshaped obstacle, and you can't locate the item (in the distance).