Hi Guys,
I've experienced the same issues on my surface book 1 + docking station. USB ports are disabled randomly and I can force this behavior by unpluging/plugin the monitor while leaving the bottom part attached to the docking station. Restarting the surface resolves this issue.
However: I reversed the way the Power Connector is plugged in and it worked immediately, Make sure the small LED is facing towards the monitor.
I didn't do any docking-station firmware upgrades.
Hope this helps some of you