Gateways operate their own schedule and set their own settlement times. This means you need to know what time your gateway/merchant account settles the transactions for the day. It is not necessarily 12 midnight in your time zone.
If you are trying to reconcile a full day (midnight to midnight), it could be off. Run the reconciliation report for the date range and break the data out by hour/minute/second to perfectly match your books with your gateway deposits. Once you know the exact settlement time, you can change the clock time when you run the Transaction Report | Cash Receipts report to balance to your deposit.