Question HDD Spinup Causing complete system freeze momentarily & SSD PCI-E lane useage

[Latios]

Ok, so i made the mistake of upgrading my machine to the X299 platform and i've had non stop issues ever since-

Todays problem is my HDD drive, its not my C drive, its there as high capacity storage for non-game related junk etc, the fault i face is when the disk powers down from inactivity, when it powers back up again the entire PC halts until the disk has spun up properly, this is something i had never come across in a computer

i have done the first rule and tried researching the fault but as always its people with dodgy installs and strange OEM power settings or something completely unrelated so i never get a result, in my instance this is a fresh install thanks to Aura sync never wanting to open with only the drivers installed, nothing else installed and nothing else changed apart from a couple things:
->Windows Defender disabled
->Paging file removed

i should explain this is a new HDD that worked absolutely perfect in my previous Z170 build with no issues

another thing i wish to ask is... my C drive is a Samsung 970 Pro which isn't slow but... i was wondering if its beneficial to have it inserted into the motherboards built-in M.2 socket or use a DIMM.2 card that fits into a DDR4-like dedicated socket as my CPU is garbage- it only has 16 PCI lanes and 8 are being used by the GPU card and another 4 are being used by a PCI x4 SSD afaik

HDD- Seagate Barracuda SATA
SSD- Samsung 970 Pro
SSD- ROG RAIDR PCI 2.0 X4
CPU- i5 7640x

 

[popatim]

Since you have your Chipset and iRST installed already,
Have you tried setting the Drive to never "Turn Off" in the advanced power options?
Some drives ignore the setting and will spin down anyways.

 

[Latios]

i tried that but.. i put this certain HDD in another system and it powers down and up as it normally does but doesnt halt the entire system in doing so