Hi Lucia,
The File Downloads report in the Links folder is a report generated when the custom link call is sent to the server containing the parameter as 'd'.
For more information regarding the reporting and the implementation, check the following articles:
As for the other File Downloads that you are seeing is a custom success event that your company admins have setup. For more information on how the success events are reported on, do read through the following articles:
For details regarding how this metric has been implemented, you will need to reach out to your developers.
Hope this helps.
-Hyder