Edit: New discovery! It seems there is something about idling that's getting to it. If I load a program immediately as after the OS is finished loading the speed is perfect and phenomenal, but if I wait for say half an hour or more before loading anything from disk it works too slowly. I suspect Windows 10 is doing something on it if it's left for idle too long.
I have a SSD as main disk drive for frequently used applications and OS (Windows 10) and a second HDD 1TB Seagate Barracuda. The SSD is fine, the problem is with the HDD. It has the exact same issue as it was with the previous unit before it was replaced.
Early on the disk was running fine for about a month or two, but recently it became slower than dirt. Any read write action would lead to 100% disk usage with barely a few KB of data transfer actually happening.
In the Task Manager I noticed it was msmpeng.exe scanning it all the time which is Windows' antimalware tool, so I added the drive into exclusions for it so that it no longer scans the disk leading to disk usage because of it, but the problem stopped only temporarily
Opening a large file like a video is so slow that the playback become choppy as the system struggles to read the file as it is being played. It sometimes becomes universally slow as in anything that uses the drive becomes dirt slow as well, including defragmentator, chkdisk, image thumbnail generation or any disk check utilities.
I used Seatools on it and passed the SMART check.
Since it was sealed packed and everything like its predecessor I don't suspect a vendor foul play yet, but rather something wrong with the configuration of the system or damage from a faulty power supply, etc.