This issue would have been there at day one.
Let's check for the more common issues.
1. Did you try a new SATA drive cable?
2. Did you inspect all cards and power supplies for BAD CAPS? (see the web about that topic for pictures.)
I have an HP desktop that was running Windows Vista that is 3 years old. It has 4 gigs of ram and a Asus A8MN2N-LA motherboard. The past year it has a problem of not booting up after setting overnight. Sometimes I receive a warning that "hard drive failure is imminent" and sometimes it says it can't find the drive. During the day I can do a restart and it boots OK. I bought a new SATA Hard drive form Western Digital and the installation went without a hitch. After about 3 months I had the same problem. I now have updated to Windows 7 Ultimate because I heard that Vista was "Buggy", but I have the same problem.. I have run all the hard drive tests that I know of and found nothing. Is there a test that will check the boot sector of the drive? I am beggining to think it's the motherboard now. So far, I have been able to boot with the windows repair disk if there is a problem. Sorry about the long post!