I run a dual boot machine at my home office, Windows 2003 Server 64-Bit on the big drive, and Windows XP Pro 32-bit on the smaller second drive. I have it set up to dual boot and it provides me with a lot of flexibility - not to mention a fail-safe way to boot into an alternate OS if I ever have a problem.
This past evening I decided to run Chkdsk. I usually do this about once a month, it's a good practice. It's a new machine and I hadn't run it before. To run chkdsk.exe properly you must set it to run on the next boot, since that's the only way it can get exclusive access to the media and be able to fix any problems it finds.
While rebooting I decided to hit the DEL key and check my BIOS. I hit the key to "Load Optimized Defaults", saved and let the box reboot.
It came up in Windows XP. That's not what it is supposed to do. Tried again--- Windows XP. Hmmm. Bottom Line, I spent a half an hour fiddling around with boot.ini, copied my backups of NTLDR etc. from the secondary drive onto the primary, and got pretty frustrated.
Finally I went back to the BIOS. When I chose "Load Optimized Defaults", it had changed the primary boot media from my big drive (Windows 2003 Server 64-bit) to my secondary drive (Windows XP).
What's the lesson? It's one I know well, and I didn't follow it:
If you are going to change something, ONLY CHANGE ONE THING AT A TIME.