There are several important details to keep in mind when balancing your daily/nightly/weekly/monthly deposits. Understanding these points will help clarify what you are looking at.
1. The transaction report is an important tool that you will use to balance your books. As you might imagine, it will show you the transactions over a period of time (today, yesterday, this week, etc.). Click here for information about some common questions that come up for people when using this report to reconcile their deposits.
2. If you are using GL accounts, be advised that the transaction report doesn't show you activity based on GL account activity. To see GL account activity, run the account distribution report.
3. If you don't see the credit card activity that you expect to see, examine the payment types section of the transaction report. It is possible that someone ran an offline credit card rather than an online credit card. If this was done by accident, and the transaction should have been run with an online credit card through your payment gateway, the payment may not have been processed and you may see more in the transaction report than you do in your gateway totals.