Well if the drives perform similar on different devices, I don't see a problem with your system.
I'd say that either your one harddrive is slowly dieing or just can't keep up with the speed of your other drive.
You could check the S.M.A.R.T values of your drives with CrystalDiskInfo. Also you could try to connect the slow drive via sata (take it out of the case) and see if it gets higher transfer rates. (that would make the one USB 3.0 case the culprit)