I just make a report out of item ledger entries to see my quantity from different entry type I can see some discripency in the beginning balance between inventory valuation and a customize report from item ledger entries by the way we used average cost for inventory valuation and automatic cost adjustment.
Discrepancy from inventory valuation and report came from Item ledger entries
If its a custom report then I would first ensure its calculating the balance correctly. Reason being that both the custom report and the inventory valuation report are getting the data from the same source.