1099-eligible vendor's payments don't all show on 1099 reports. How can I bring all of the vendor's payments into the report?

What type of transactions are your payments?  Checks? Cash? Are they all the same type of payment transaction?

Do all the payments use 1099 mapped accounts as the expense accounts?

brconsultingid2is correct, davetodd.

Although the payments are taxable and associated to the vendor, there are some that don't have to be reported on Form 1099-MISC. You can visit the Exception section Page 2 of the Forms 1099-MISC guide link.

We'd recommend reviewing the payment methods of the three payments.

1. Click Vendors at the top menu and select Vendors Center.
2. Highlight the vendor profile and double-click the bill payment.
3. Make sure the BANK ACCOUNT used is a bank account.
4. Click Save & Close and select Yes to confirm the action.

After that you can go back to the 1099 Wizard and continue the process. Make sure to map the expense accounts correctly. Here's an additional reference that you can use: 

Prepare and file 1099s with QuickBooks Desktop.

We're here to ensure that you file your forms without delays. Have a great day!