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1) please check whether you are using the correct bank statement for reconciliation in case if you have multiple bank accounts / Statements.
2) Check whether the payments that were unreconciled were all functional currency or foreign currency payments ...in which case exchange rates might be causing this ..
References:Autoreconciliation Execution Report Shows Exception No Matching Payment Batch [ID 166716.1]
Autoreconciliation Has No Matching Payment and No Matching Payment Batch Errors for Foreign AP Payments [ID 1387334.1]