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I don't think FreeDos version is the problem. Once Amithlon is launched the stripped linux kernel kicks out the running OS and takes over the hardware, remapping PCI address space among other things.
I'm really not sure what the issue is you are having. This motherboard was recommended to me from a long time Amithlon user and after setting it up and comparing against others it has been my recommended board. I run two SATA hard drives and one IDE DVD drive (Amithlon's kernel does not support SATA optical drives).
If you have the motherboard manual (download it if you don't), there may be weird SATA/IDE mapping in the BIOS and you'll need to use specific motherboard connections? It's been a number of years since I physically setup this board but I will see what connectors I'm plugging my SATA drives in.
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