If you are facing any reconciliation discrepancy in QuickBooks, either you can contact QuickBooks tech support at +18772499444 to get the proper help or you can try to fix it on your own.
First option is to undo last reconciliation until you get back to the last month which was reconciled correctly. Second option is to ignore the beginning balance in the reconcile window, enter the ending date as well as balance for the month which was reconciled properly. Continue till you avail the balance zero and then start reconciling the other month.
The best is to get Quickbooks tech support from the team so that the issue gets addressed properly.