When viewing the Generate payments page the data list that contains all of the processes does not have site security. Users are not able to assign a specific site to a Generate payments process so it only shows for that site in the data list.
We are currently evaluating this issue and will update this article when we have more information.
Steps to Duplicate
1. Navigate to the Revenue functional area. 2. Under the Processing heading select EFT. 3. Select Generate payments. 4. Notice that you cannot assign a site to a Generate payments process. A user will be able to see all processes in the data list regardless of their assigned site if the user has feature access to it AND they have access to the Account System that is used on the process.