Your message says "disabling joysticks" . Try moving the Joystick.dll out of the folder. Are you using a Microsoft controller?
Things to check
1. Test controller. For Microsoft Go to Control Panel, Devices and Printers, right click and select "Game controller settings". select Properties and then select Test. Other manufacturers should include their own test programs.
2. Copy Mach3 (entire folder) off to a safe place. then uninstall Mach3 and reinstall it. Then copy the XBox360controller.DLL into the plugins folder. Then try that.
The 2 tests above will determine if the problem is with the controller or Mach3. If it passes the 2 tests above then the problem is in software. Some files (DLLs) that are needed are not on your computer. As Microsoft has moved forward, they have replaced some DLLs with new DLLs of the same name and the new ones are missing some calls. They have also not included all the files needed. It can be tough to find the missing files.
One more thing you can try is to go here:https://www.microsoft.com/hardware/en-us/d/xbox-360-controller-for-windows?refid=12
and install the appropriate version of the controller software (64 bit or 32 bit). That will add in any drivers for the controller that you are missing.
Another possibility is security. If you are not an administrator you may not be able to run some things. But, I assume that you are or you would not have been able to install the DirectX runtime.
If none of the above solve the problem then you may have to go and get an older copy of the Net Framework (such as 2.0) and install it. It will also copy in older missing files. But, I don't feel that you should have to do that.
Keep me posted.