Each time a payment is received from Centrepay, $0.99 of the deducted amount is kept by Centrepay. If the Tenant organises a deduction of $200 per fortnight, Centrepay will keep $0.99 of it meaning that your organisation will receive.$199.01. Chintaro will show that the Tenant paid $200 but the $200 amount will never be received into your actual Bank account.
Instead, Centrepay groups payments of different types into larger amounts - less the $0.99 fee for each one. This makes it hard to reconcile the total rent you received from Centrepay for each day with the amount you actually received into your bank account because if you try to reconcile the amounts you received in your bank account with the rent payments from Centrepay, you will be $0.99 out for each payment received.
So you will need to find the total of fees withheld by looking in the View Bank Accounts screen and selecting Centrepay as the bank account. Using the column filters, you should be able to filter the date range you want, and then use the filter on the Description column (containing "Centre" or the like) which will give you a view of all the Centrepay fees for the day. Using the Export button in the top right corner, you can open these in a spreadsheet and add up the total.
NB - If you don't have the column filters or the Export button, you will need to update Chintaro.
Once you have the total of the Centrepay fees, you can use the same method to find the total of the amounts received for the day (by filtering the columns in your actual Bank Account).
These two amounts added together should equal the total of the Centrepay Payments processed into the Tenancy Ledgers. To find that amount go to Finance>Tenancy Transaction Functions, Manage Tenancy Transactions screen and filter the Transaction Type to Rent Payment, the Date column to the date range you are after, and the Comment to Containing "Centrepay" you will get a list of all the Centrepay Payments made for that day. The total dollar value for those fees will show at the top of the screen.
You can also export from this screen if you want a spreadsheet containing all of the transactions.