I had problems flashing ANY firmwares on this machine I just built, including the NEC 3500's. I'm not sure exactly WHICH step cured that issue, as I was trying to resolve a couple at the same time, but after I'd re-loaded XP Pro a bit differently, then I was able to flash the MoBo's bios, and also the NEC's using either the DOS utility, OR the windows flasher. (Liggy's OR NEC's) I'm sure that while flashing the drive in an external enclosure worked for the time being, you'd still like to be able to flash the drive with the machine that it normaly resides in. Therefore, I just thought I'd chime in and see if perhaps this information was of any use to you.
If you've not done so, I'd recomend flashing the MoBo Bios to the latest available version.
Look carefully through your bios. I found not only a setting to enable or disable DMA on the HDD controller, but also later found a setting to set PIO settings and UDMA settings manualy. This casued me problems before I found them.... although flashing the drive was not one of them. This setting was under the "Advanced" tab in a Phoinex/Award Bios, from advanced there is a setting for "SB200 IDE controller" or the like. UDMA settings available are AUTO, 33, 66, 100 or OFF. (Mine had been set to off.)
Hope that helps you, or SOMEBODY.