I was using a USB 3.0 port with an aftermarket USB-C cable that was almost twice as long. (I have been using that longer cable this entire time though, so I am not sure if that was the issue).
It could also be a problem with the port. I have a laptop with a blue USB 3.0 port, and probably 7 out of 10 times I use it it fails. I'm not sure what is happening on the Switch when this happens either, but I can't try again without holding the power button for 10+ seconds and going back into RCM. When I'm on the go, I've just gotten used to attempting several times to start my Switch.
I also have a desktop computer with a USB 3.0 port. Same software, same driver, same cable. Works perfect every time.