If you do not tick the second box in maintenance specify window, then it OKes the stock updating records in date order, and within each date it first OKes Productions, Goods Receipts, Returned Goods, Returned Goods to Supplier, Stock Depreciations, Deliveries, Stock Revaluations, Stock Movements, Work Sheets

regardless if your stock valuation method is configured as FIFO or Weighted Average and if you do NOT have chronology turned on, and users have been backdating stock updating records, rebuild stock with only first box ticked will most certainly change values in stock list reports, because it is recalculating the order the items go out of stock