We have only tested using USB 3.0 built into the Mac. Our USB 3.0 devices are complex USB devices with many end points. They are USB 3.0 compliant, but can expose bugs in USB 3.0 host controllers. In the past 12 months we have gone through a lot of work with the host controller vendors getting them to fix the issues we have exposed. This has included Apple, who fixed bugs in their USB 3.0 controllers before we enabled support for our USB 3.0 devices.
It is most likely that this is due to a problem in the USB 3.0 PCI Express card. I would check for updated USB 3.0 HC drivers. If that doesn't help, I would suggest using the dock through USB 2.0 for stability.
Wim
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