It is possible that your chipset is not compatible to flash the drive. This really happens a lot. Most users here will advice you to use/buy a via 6421 chipset card (almost always works) or a x360 usb prob wich will allow always flashing from pc or laptop.
If your pc is up and running and you should connect your drive, power the drive and then start JF with admin rights, it should recognize the drive. if not i advise you to get your hands either on a via card or usbpro. Make sure that you refresh your com properties in JF and pick the right com port. Don't know if you already done all, but just to be sure...Good luck