It could be a bad hard drive, some die quicker than others, even when there is no S.M.A.R.T. errors, sometimes drives just do not function well enough, even S.M.A.R.T. may not detect these problems. I have an older WD drive where i generally have to check the bios during startup to see if it's there and let it sit before restarting because the drive takes a minute to warm up. Do you hear any weird noises coming from the drive when it does not show up in bios or your PC? A couple of reasons why this problem might exist. Either the drive is struggling to turn on from a cold boot, a short somewhere on the board maybe, loose connections, bad motherboard sata port, power connection or your PSU is not providing enough power during a cold boot.