OK cool so you understand that you shouldn't use that system for freenas? Only having 1hdd is not the point and you should just use a usb attached external drive.
Where is it written that FreeNAS MUST be used with multiple hard drives in a RAID array? FreeNAS appears to be perfectly happy operating with 1 drive for the OS and 1 for storage, aside from this one problem. (A problem which, admittedly, is unlikely to be FreeNAS's fault. But this certainly seems like the first place one might go for some insight, no?)
I don't understand the point of this rigid adherence to massive storage arrays if the OS works fine on lesser systems. "Good choice for use as a FreeNAS box" is subjective. Everyone's needs (and budget) are different. Just because FreeNAS is all but infinitely scalable doesn't mean it HAS to be used for massive RAIDed storage applications.
Anyway, this seems more like a philosophical question and I'm not interested in some old school nerdier-than-thou flamewar. Clearly I'm not the only one having the problem at hand, and not everyone who's having this problem is using an all-in-one mini PC, therefore the problem is not necessarily the choice of hardware. My personal FreeNAS box (with a 12TB ZFS2 array, for you sticklers) only has HDMI and DVI on the mobo and it works fine as a headless machine, for the record.
I'm here asking about my car making a funny noise and you're telling me I shouldn't have bought a Toyota. That's about as unhelpful as it gets.
I will try some flavor of live Linux off a USB thumb drive or something, just to see if I get the same result (indicating it's a BIOS issue). So thanks for that suggestion anyway.