Recommend checking:

- Computer System's BIOS configuration for the large drive. There may be a few different settings there that affect the drive's performance. For instance, I have a computer here at work where I have to disable the "SATA BIOS ROM" feature in order to get the system to boot from the CD-ROM, but it makes the hard drives dog-slow. So I re-enable that feature in the BIOS after I'm done with whatever I needed the CD-ROM booting for.

- Make sure you have the latest Windows OS device drivers updated for the motherboard, SATA controller, PCI chipset, and perhaps even the drive itself.

- Rule out the external USB drive as a factor. Copy (not move) a single very large file to another location on the same 3TB hard disk. Is that really slow, too, or is it lightning fast? If so, then I would guess the problem is the external drive and/or its enclosure, not the 3TB drive.