Amazon's MWS API applies (resets) the default Fulfillment Latency when stock is pushed unless latency is provided while updating stock. It is common for APIs to set defaults when specific values aren't provided. It would have been great if Amazon MWS API left Fulfillment Latency you set on Seller Central as is because this creates a problem for a lot of sellers such as yourself.
To solve this MWS API limitation, SKULabs allows you to set latency per-item and kit basis. This can be done from the item/kit edit window or via CSV.
If you're would like to update multiple items in bulk using CSV, use:
Items details CSV import - include only SKU and Latency column
Kits CSV import - include complete kit and component items information plus Latency column