@Bas, did you connect a USB-2 device to a USB-3 port or were both the device and the port USB-3?
usb-2 ttl-to-serial devices are quite common. usb-3 ttl-to-serial devices are not common or perhaps are nonexistent.
Non-FTDI cable (works great): https://www.adafruit.com/product/954
FTDI cable: https://www.adafruit.com/product/70
It seems that if a USB-3 port (PC-side) does interrupt time-stamping, then it shouldn’t matter if it’s a USB-2 or USB-3 device.