The Qty On S/O is the sum of the open orders.
As you are on an older version of OE, you have only just noticed this problem, and no one has complained about this issue, then something has changed in the way you use Adagio or your Adagio setup.
It could be a timing issue. Check to see if the difference is the Qty shipped not costed. I believe you will need Adagio Reports or GridView to see this number, its not on the Item Inquiry.