This can occur if you use unit of measure that is multiples of one other unit of measure. For example, on the transaction you may sell the item in quantities of a Unit of Measure called 'pkg' that is 5 'each'. If you create a transaction and add a line item with the quantity of 1 pkg in Quickbook, it will sync over to Method as 5 quantity on the transaction line. If you create a transaction in Quickbooks with a line item with quantity of 2 pkg, it will sync over to Method as 10 quantity on the transaction line.
The cause of this issue is due to the limitation of the Quickbooks SDK. Quickbooks is sending the quantity field without consideration of that Unit of Measure.