Do you at least know if it's a USB2.0 or 3.0 drive? Are you using USB 3.0 ports?

If it plays from the hard drive but not a flash drive, it sounds like the read speed of the flash drive could be too slow.
Try the speedtest on USBdevview and see what you get.
http://www.nirsoft.net/utils/usb_devices_view.html

mp4 files aren't all the same. Just because some files play, that doesn't mean all mp4 files will play.