It happened again today for the first time in months. Interestingly, my external was plugged in at the time, which it usually isn't. I was also using my external a lot when I was having this issue back in January. I think this is definitely more than a coincidence. It seems that having the external hard drive plugged in during boot interferes with the internal HDD being detected. Any idea why this might be?
Just to update this thread: I fixed the problem, and the cause was the last thing I would have guessed. It was the CASE! After spending countless hours talking to my HDD, motherboard, and eventually case manufacturers, I found the issue. Apparently, there was some sort of grounding issue caused by the metal standoffs on the case that the motherboard is mounted to, and for whatever reason this was causing problems with HDD detection, and even causing the CPU to get stuck at POST sometimes.
I took all the parts out of my case and assembled them on top of a piece of cardboard, and now everything works perfectly. I just have to decide what I'm going to do with this case now.
Quote