I don't think it matters which drive bay you put the drives in. (The drives bays, BTW, are not "hard wired" to any specific SATA port assignment. Bay #1 can be SATA port 1 or 2...same with bay #2.....and they can even swap when you reboot!)
But it's worth checking the drive's alignment, because of its history of previous use. Just deleting a partition doesn't assure proper alignment when new partitions are made. The Diskpart utility is the easiest way to check....the steps are listed below. All command line commands are in quotes...omit quotes when actually typing using them. (Let me know if you want more detail for any step).
- In Windows, open a command window as administrator
- type "diskpart" to open the Diskpart utility
- type "list disk" to get a list of your physical disks, each assigned a disk number
- type "select disk n" (where n is the disk number of your SSD)
- type "list partition"
All partitions on the SSD should be listed, with the following data specified. Please report back with this data.
Partition #.....Type.....Size.....Offset
Type "exit" to close Diskpart, and then "exit" again to close the command window.