I have tried two different XBMC versions (OpenELEC and XBMCbuntu) trying to get my Zotac Zbox AD03 computers set up as HTPCs. In both dases the install went very well, I got the system running and was very satisfied. I had also rebooted each computer from the system a number of times. However, when I shut dosn (power off) the drive disappears from the BIOS boot table. I've tested both drives and they are healthy. In fact both will boot in my regular desktop PC.

I guess I'm grasping at straws trying to find a reason why those particular computers cannot see the SSD after a version of Linux is installed.

Seems to be a common issue. Bios has nothing to do with (normally) the OS. In some odd cases you don't need bios to see all drives but you need it to see the boot drive.

See web pages on how to fix this issue. I think it ends up with a get new motherboard or ssd or both.

If you think it is possible that linux has somehow changed bios settings then be sure to try some different or older distros.

Guess it can't hurt to change the cmos battery.