Ok that seems kinda strange, if your board is a gigabyte 965P-DS3P then it should have them as both revision that i'm aware of as being sold over here have them.
Rev 2.0 http://www.gigabyte.com.tw/Products/Motherboard/Products_Spec.aspx?ClassValue=Motherboard&ProductID=2418&ProductName=GA-965P-DS3P
and the later
Rev 3.3 http://www.gigabyte.com.tw/Products/Motherboard/Products_Spec.aspx?ClassValue=Motherboard&ProductID=2455&ProductName=GA-965P-DS3P
So what i'm wondering is what board it is you have exactly?
I've had previous problems having samsung drives running in AHCI in concert with other brand drives on 965 gigabyte boards, we fixed it by changing back to IDE mode thats why I suggested it.
Ok I also am assuming from what you said before that your boot drive is the Samsung 500GB? As a rule at work we always connect a hdd (usually the boot drive) to the 0 connector on the sata controller as that way its seen as the Primary Master drive. I;m not entirely sure it makes any difference on that board but it has been known to on some of our other brands. Yes its not an issue to change where the primary boot disk pointed to in bios, but we have had issues in the recent past where one of the other techs had a samsung sata burner the (202, 203 whatever it is) in position 0 and we had issues with drive throughput during the install with the harddrive connected to port 1. Was on a 945 based MSI board switching them fixed it.
Dodgy cables again tend to cause random spin down spin ups when transferring, but again from previously stated i'm assuming you've tried that.
So yes otherwise all I can think of is that Vista is being crap (as usual) in its copying procedure and is causing it.
The HDD has a fault, we've had samsungs returned before with random spin downs, but it would spin down quite often, regardless of what the system was doing at the time. In which case usually the disk will fail the long drive test in the samsung disk utilities.
Other investigation, try running HDTach (large block test)or similar to look at the read/write speeds across disk which could shown an indicative low spot where the drive has issues reading/writing again a hardware issue.
Running the HDtach on another machine with say XP would also eliminate the vista part of the equation.
I'll mention this to one of the other guys at work tomorrow to see if they can recall anything more about the previous disk with the spin down errors.