I bought a Supermicro server with 823T-550 chassis and PDSM4+ motherboard on 4th December 2006. The Server came with 2x80GB Seagate SATA and 4x200GB Seagate SATA. The 2x80GB SATA were RAID-ed using the on-board Intel ICH7R RAID controller at RAID 1 level. The other 4 hard disks were RAID-ed as RAID 5 using add-on Areca RAID controller. The server is running Windows 2003 with sp2. The OS is residing on this RAID 1 volume. The server failed to restart for the 1st time in April 2007, and after thorough investigation, I found that it lost its RAID configuration for the on-board RAID, as if at the state when the server was just setup, not yet configured RAID. The vendor then changed the motherboard. I re-created the RAID, restored the OS. In May 2007, it happened again. This time the vendor took the server back, and did a firmware upgrade. After that, the server was running OK until 5th of May 2008, it happened the same problem again. The break of the RAID happened during restart because while Windows was still running the RAID must still be intact, else it would have blue-screened. Many people said this thing is not possible, but here it was real, and happened 3 times already. Any suggestions?

I've run into a very similar problem.
It's an Intel ICH9 board using onboard raid 5, had to replace the board because for some reason it started hanging on post with a keyboard error if no ps2 keyboard was attached. (used the diagnostic leds to decode).
The controller showed the drives online with the hotspare and it booted once to windows.
I rebooted it and suddenly the entire raid was gone, pretty much exactly how you describe.
So I'm going to be watching this thread with interest.