The issue is probably on their side, usually when EPDM sees a Toolbox file that is not part of EPDM's Toolbox, EPDM will swap the "offending" Toolbox part out and will substitute it with one of its own.
Kinda like white blood cells attacking a foreign substance in the assembly.
This behavior can be confirmed if they open the assembly and look at the referenced file to see which set of fasteners it is using.
This is an expected behaviors although you have sent the tool box components along with the files.
SolidWorks always try to browse the tool box components from default location.
As a work around what you can ask the customers is Close all the SolidWorks files then go to tools>options>Hole Wizard/ToolBox.
Un Check the option 'Make this folder default search location for Toolbox component'.
Try opening the files & check the behavior.
Hope this helps !!!
If you go into the SolidWorks installation directory and go to the \Toolbox\data utilities folder you can run the sldsetdocprop.exe application.
In there you can set the toolbox flag to No. This will remove the files from being replaced by Toolbox files.
You can add all the files at once and set them all to "No" then update the status.