Occasionally, when you have updated a couple of Profiles in QuickBooks (Desktop), those profiles/transactions will not come into the Integration window. This may be employees' direct deposits, vendors' bill payments, or customers' collections. All other transactions come over except the one or two Profiles where changes were made.
You may want to first double-check that all of the transactions are using the same bank account that is connected to ACH Universal.
Try the integration using the Sample account. If all of the transactions come over into the Integration window using the Sample account, your production database in ACH Universal may be corrupt. If using the Desktop platform, you can Restore a Corrupt Database
If the integration does not work in the Sample account, then go into the QuickBooks [Employee, Vendor, or Customer] Profile, and review the Bank Account Number and ABA Routing Number to make sure
--there are no spaces before or after the numbers entered
--there are no special characters in an account number
--the numbers are not reversed (in the wrong fields)
If you are still unable to transfer the transactions for those specific profiles/transactions into ACH Universal, you may have an indexing issue in QuickBooks.
You will want to back up the QuickBooks .QBW file.
--File > Backup Company
Then, run a Verify and Rebuild process: (This reorganizes the file indexing.)
--File > Utilities > Verify Data
--File > Utilities > Rebuild Data
If you are still unable to bring over the transactions, you will want to use the QuickBooks File Doctor app.
If those few transactions will still not come over, you will want to consult with a QuickBooks Pro Advisor, or call Intuit Support for assistance with troubleshooting.