Does the In Stock quantity update type look at all inventory columns?
The In Stock quantity update type does not account for the Pending Shipped column or the Pending Payment Cleared column. It will subtract out quantity allocated to open auctions and items pending checkout. For example, you have SKU A and there is 1 open auction, 1 pending checkout, and 1 pending shipment. You then update the quantity using the In Stock type and set the quantity to 25. In this case the 25 will subtract out the 1 open auction and 1 pending checkout and set the Available Quantity for SKU A to 23.