I believe this problem started happening when I returned my bios settings to default. I sometimes get the “operating system not found” error. My machine is a Supermicro 6015B-T with windows server 2008. I reinstalled the OS but ended up with the same results. After some googling I found out about “hard Disk Pre-Delay” which would make the bios wait for the hard disk to be ready, but I don’t see that anywhere in my bios settings. Is there anything I can change to prevent this from happening?
EDIT: when I have the windows server disk in the machine it almost always boots up since it creates a few seconds delay before trying to boot from the hard disk.
Your symptoms make it sound like the hard disk, particularly the MBR/GPT area, are sporadically unreadable. I recommend doing a thorough disk scan with chkdsk or the tool of your choice and preparing for the possibility that the drive is failing (doing backups, getting a new drive ready if it is needed).