Are you using FX3 SDK v1.3.4?
I checked SDK v1.3.3 and everything is fine here.
I found the solution. The file /etc/cyusb.conf did not exist. I was attempting to make the installation work with just user-mode files, so I did not copy files to the /etc folder.
There should be a warning if /etc/cyusb.conf does not exist or is not readable! There was another discussion on this website with the same failure mode that went away when the user ran as root. It is probably a file permissions error, where /etc/cyusb.conf was not readable.
The alternative is that the fx3_download application should take VID and PID arguments so that /etc/cyusb.conf is not necessary.
Thanks for your suggestion. I will update it to software team.