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First, you also need fast CF cards. 60MB/s cards (400x) will only read at said speed. 600x or 1000x cards should read faster.
Separately, make sure you're using a USB3 cable. It sounds retarded, but USB2 cables won't work, even though they are identical pinwise. Make sure your cable has the blue USB3 connectors on it and is connected to the blue usb3 connector on the motherboard.
A USB 2.0 reader will only read at about 30 MB/sec., so the difference will be apparent with anything faster than a 300x card.
The USB 3.0 cable "A" connector has the USB 2.0 connections, but also the separate ones for USB 3.0. In any case the "B" end is clearly different. A standard USB 2.0 cable (D connector on the B end) will work on a USB 3 device, albeit in UAB 2.0 mode.