I was having the same issue. I have an Asus X99-AII motherboard. It all started happening when I updated to the new firmware just a few weeks ago. There must be some sort of power saving feature knocking down the USB port speed or something, enough to interfere with transfers the Vive needs. Here's how I fixed. I moved the USB for the link box to a USB 3.1 port away from all the other USB ports in use. It detected and reinstalled the Vive usb drivers and walaaa! Havn't had an issue yet. Hope this can help a few people. Also I was going to go check in the bios to see if there was a USB or some sort of power saving feature I could turn off in bios. Also to note, I am overclocking my RAM and you should check to see if your board automatically overclocks the memory and compnents. Asus deffinitly does this right out of the box wthout you knowing. It will enable XMP right away most often. My I7 6850k was overclocked to 3.8ghz up from 3.6 on all cores automatically. This CAN cause issues so make sure to check, especially your bootstrap setting. It should be at 100mhz. Check.
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