Where did you check for the Scrap percentage? Material Master or BOM or Routing? Double check your routing details if you had not done earlier.
FYI the Qty adjustment field is checked ON or OFF (default setting) to instruct the system on how to take into account the scrap percentage of each earlier operation/s when we do a final/mile stone confirmation.
What we see is you are doing a confirmation per operation and system would purely go by the scrap percentage given in routing operation level and the setting has no relevance at all.
Read this SAP help page to get more clarity:
Generated confirmations w/o quantity adjustment
(Just realised that we have skipped from your original topic and we are discussing a new topic as of now. Please start a new thread for your individual queries in future).