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I just bought a new 3tb HGST drive. When I plug it into a usb3 dock I’m getting transfer speeds of 160Mb/s which settles around 115-120Mb/s.
The same drive plugged in internally via SATA 6G/s connection starts at 100Mb/s and settles around 70Mb/s with dips down to 30-40Mb/s

This is a Windows 7 machine with 4 internal drives. I can’t find any driver issues. Or anything that would be throttling internal drive speeds.
It’s not an issue with the drive since it’s the same drive I swapped from the usb3 dock to internal sata.
 

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Can you check the Motherboard website for SATA Controller updates ?
 
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