Are you using 2.4GHz wireless networking? This can interfere with USB 3.0 (they share the same frequency range) and vice versa. Try disabling wireless networking and bluetooth and see if this alleviates the issue.
Hope this helps,
Using Samsung Magician I've found my external SSD Drives register as being a 2.0 USB rather than a 3.0. Using that exact program on a NUCi5MYTHE unit running Windows 10 Enterprise it sees the USB SSD's as 3.0. I'm not sure if this is a driver issue with Windows 10 E, I'm about to wipe one of my NUC's and test 8.1 Pro with it's correct drivers and see if I get a difference.
So in short, I don't think that's the issue at all.
Here's soemthig to try: Go into Visual BIOS and use the F9 key to restore the default configuration. Then, only change those few options (like SATA Mode, UEFI Mode and Boot Order) that are needed to boot successfully. Boot into Windows and test the USB performance again. Do you see a difference?