Seagate's tool is not really running in a very different manner. Whether you download it from Seagate's website, or boot it from UBCD 5.1.1, it is used under FreeDOS. So my guess is that you would need to add some DOS driver for the card
Have you tried asking in Seagate's forum? Maybe there is a different tool, better suited for your hardware, or any other alternative way to test the drive in your specific hardware (knowledge useful also for future cases).
If you get any info, please share it here too.