Hi Russ,
Since you've got the HDD popped out, you might want to try running CHKDSK /R against the system and data partitions. If you have SMART monitoring software on the PC being used to check the disk, have the SMART utility examine the disk. You can use HD Sentinel (hdsentinel.com) -- you can download a full-featured trial version (it actually will run forever but nags you)...this can check most USB/FireWire enclosures in addition to internal disks. This tool will tell you if the hard drive has reported any internal failure conditions (i.e. bad sectors, end-to-end errors, spin retries, etc).
Assuming your HDD comes back perfectly healthy, then you can move on to the BIOS.
An item talked about a LOT on this site is the VOV Gen3 debug cable. My advice is that you get one:
viewtopic.php?t=8066This cable turns any HP MediaSmart Server and the Acer WHS from a "headless" box into one with full keyboard, video and mouse capabilities. It's a bit pricey ($80 USD for the video + PS/2 keyboard/mouse), but the time it'll save you is well worth the $80.
My gut instinct is that somehow the boot order has gotten screwed up and the server is booting from the built-in USB flash. My EX487 likes to do this; I've found that if I change USB disks (including leaving a flash drive plugged in the front port) and reboot the server, the BIOS lovingly (and magically) reorders my disks and somehow the built-in flash hops to the top of the boot order! Without the debug cable, I would've never been able to fix this.
In my 20+ years experience working with computers, I have NEVER seen a BIOS just die. I've seen a few killed due to a botched BIOS flash, but if your BIOS just up and died for no reason, it'll be the first (for me). Without a debug cable there's no way to tell, unless you knowingly tried to flash the BIOS right before the trouble started, in which case the BIOS flash may have failed.
Shoot Charles an email, per the instructions in the linked article. He ships fast upon payment, and expedited shipping is available. I have two--the one I ordered more recently I requested on a Monday--the next day I got the invoice which I paid promptly and I had the cable by Friday. My EX487 and EX490 are both hooked to a KVM and so I never have to worry about troubleshooting blindly anymore.