Faulty BIOS or Faulty SATA Controller

At first I thought I had an HDD problem. About two weeks ago my computer just froze and I was forced to improperly shut down. Upon restarting, I couldn't load up Windows Vista. I could get into BIOS and I could attempt to run a diagnostics of the system (a feature of my HP Media Center), but I could never get beyond that. It was giving me the message about inserting a disk or setting up the proper boot order. So I check BIOS everything is set correctly however no HDD is detected. And come to think of it, neither was any other device (DVD Drive for instance). Both DVD and HDD are SATA connections. So I order a new 1TB drive (different brand with good reviews to be on the safe side). Two weeks later (or today) I get the new HDD, plug it in and am getting the same exact problems.

So really what's happening is that sometimes HDD and DVD are detected, but I can't load an operating system (whether installing or booting to) and every other time nothing is detected in BIOS. So I'm thinking I have a problem with the motherboard. I mean as far as I can tell everything else works fine because CPU and RAM passed the diagnostics test. I have been reading around and I've seen all kinds of suggestions. Flashing the BIOS, Resetting BIOS, that I have a faulty bios?, or a faulty SATA controller. I tend to think that it's that last one. Something must be wrong with the SATA connections on the motherboard.

Anyway, I was hoping someone would have some answers before I go ahead and buy a new motherboard. Because I'd really rather not buy a new one after buying a new HDD that I probably didn't need. Thanks in advance.

 

Let's start with the basics:

Please post the make and model of the motherboard, the DVD drive and both hard drives.

Whilst you are in the case let's start with some basic troubleshooting: Disconnect and reconnect the SATA cables and the power cables. Make sure none of the connections look damaged or overly worn.

Also remove the CMOS battery on the motherboard and leave it to sit for 20 minutes or so, then replace the battery and try again.

 

Sorry, I should have added that I have already checked connections many times as well as removed the CMOS battery. I even bought a new Serial ATA cable to see if that was the problem. None of these things consistently fix the problem, meaning I have gotten the BIOS to detect the devices a few times, but upon saving settings and restarting, they disappear again.

As far as the models of everything goes:
Motherboard: M2N78-LA

DVD Drive: HL Data Storage Super Multi DVD Rewriter Model:GH10L

HDD Original: Seagate Barracuda 7200.11

HDD New: SAMSUNG Spinpoint F3 HD103SJ 1TB 7200 RPM 32MB Cache SATA 3.0Gb/s 3.5"