system recorded deposits

Let's figure out why these deposits don't show when you reconcile the account,  T McMichael1.

The deposits in the Deposits from QuickBooks Payments page will automatically affect the account register if you have set it up in the Account and Settings.

1. Click the Gear icon in the upper-right corner and select Account and Settings.
2. Select the Payments tab and go to the Chart of Accounts section.
3. Ensure that the affected accounts are correct in the Standard deposits and the Processing fees fields.
4. Click Save and Done.

The changes will only affect the future transactions. If you did not set this up before, the invoice payments will sit in the Undposited funds as the default account. With that said, it won't affect your account register and also the reason why it is not showing in the Reconcile page.

To correct the existing invoice payments, we'll need to deposit them manually.

1. Click the + New button in the upper-left and select Bank deposit.
2. Select the bank account in the Account field and the Date of deposit.
3. Go to the Select the payments included in this deposit section and mark the payments.
   You can deposit them at once or one at a time.
4. Click Save and close.
   You can use this link for reference: Record and make Bank Deposits in QuickBooks Online.

They should now appear in your account register and in the Reconcile page. From there, you can continue reconciling the account.

Please let us know how this goes so we can further assist you in correcting your data and reconciling the account. Have a great day!