Unusual Hard Drive problem after upgrade.

[NeptuneUK]

My new motherboard keeps having issues detecting my main SATA hard drive.
Plugging both my main 1TB and extra 500GB SATA drives in at the same time makes the problem worse. Every day since the upgrade I have to restart the PC several times before the hard drive is detected by the BIOS.
Today I have spent 4 hours trying to get it to work with various SATA cables and BIOS settings. This is the second time I have booted it. Last time (approx 40 mins ago) I was stuck restarting the PC until it was magically detected.
I have put the hard drive into my old motherboard and it boots up with no issue. Scandisk couldn't find anything and there are no SMART errors.

I have a Samsung spinpoint F3 Hard Drive and a Gigabyte 990XA-UD3 Mobo.

Edit: There seems to be a firmware update from samsung that improves compatibility on the SB850 chipset, but I am running the SB950. Anyway I would assume in this day and age I wouldnt need to download something to make a hard drive work!
I need to boot the system up in DOS and run an EXE file. I've not had to do this since the days of floppy disks. How do I do it with a USB drive?

 

[Unfocused]

Doesn't the firmware update come with step-by-step instructions on how to run it (since doing anything in DOS is pretty advanced nowadays)?

Do you have to run it from a USB drive? Perhaps you can put the exe file on your system drive and run it in safe mode with command prompt.

 

[NeptuneUK]

It came with **** all instruction. Samsung was like "here is your update exe, have fun!"
I finally managed to do it by producing a makeshift PC on my table with old parts because the HDD just wouldn't detect on the BIOS and updating via bootable dvd with appropriate exe file and corresponding DOS software (Volkov Commander). It's 8 hours of my life I'll never get back.
The USB method would simply not work and I shamefully have no CD writer so had to burn one from a borrowed laptop.
The fact that I had to update the firmware of a hard drive in 2011 to make it work with a particular chipset is simply absurd in my eyes.
The funny thing is, If I had a floppy drive and a spare PC it would have probably taken 15 minutes.

Edit: I guess though these sort of bullcrap, ballaching problems are the sort of things that you get when being a PC enthusiast for many years and I can now be content with my new system. I'd hate to admit it in retrospect, but wiring up a makeshift PC on a table and coming up with the required workarounds was sort of fun