Hi Bushman. A payment made in 1-1 where you select an existing Vendor will record the payment in the All Payments window in 4-4  and go against that vendor's 1099 balance. This however is not the case if recorded directly in 1-3.

You must use the vendor field (not payee) to link the 1-1 checks to the vendor to show up in ALL Payments button.  You also cannot edit those records because then they become a journal entry and will not display even when attached to the vendor. 

I have submitted an enhancement request to include those records in 1-3 that may have come from an edit or journal entry as long as the banking category is set to check.  But it hasn't been implemented yet so please search and vote on it.

Ghollister - That was the problem!  1-3 was being rolled forward and used copy after copy instead of using 1-1.  Great catch and answer!  Thanks!

I think the editing is part of the problem.  I love the 1-3 enhancement request.  I'll vote for it, but not sure how to search for it?  

Editing a payment transaction that was entered in 1-1 (Source is 1 - GL Check) should not remove the payment from the vendor's 'All Payments' or 1099 balance

It had in the past, so that was resolved?  And what about users who still enter them in the 1-3 but then mark them as the banking category of check.  We have a lot of users setting up the automatic payments in 1-4 and posting them.  Those need to show up in all payments as well.

Here's the way it works in the current version (26.1), assuming a Vendor has been selected in the Vendor field:

• Payments/credits to a Vendor posted through 1-4 Recurring Journal Transactions will be included in the All Payments window in 4-4 and will update the vendor's 1099 balance
• Payments to a Vendor posted in 1-1 will be included in All Payments and the 1099 balance
• Payments to a Vendor posted directly in 1-3 will not be included in All Payments or the 1099 balance
• Editing a transaction in 1-3 that was posted via 1-1 or 1-4 will not delete the payment in All Payments or remove it from the 1099 balance, but if you change the amounts in the lines, it only updates All Payments, not the 1099 balance. To adjust the 1099 balance, you will need to go to 4-4, pull up the vendor, and go to Options > 1099 Balance/Startup Adjustment

I believe these things have been like this for a while as I have no record of any fixes in this area in the last several releases or updates.