After more fiddling with the NAS, including putting in a graphics card so that I could add a monitor + keyboard to diagnose the problem, I am tempted to blame the S-ATA controller itself. The bootup starts, finds the memory ok and my cdrom, but on the next screen I am getting : "Warning - the bios does not find proper hardware configuration, please check your system again!"
Another suspect I had was the Motherboard, but alas, this is probably not the case. I tried to connect the S-ATA controller to another Motherboard, and I got the exact same thing there.
One last thing to note: after about two minutes the message dissappears and it finds three out of four hard drives and Naslite-2 starts booting.
So do you think that my eight month old S-ATA controller is about to die or am I doing something wrong?
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