I'm using Pixhawk 2.1 and Windows 8.1 laptop.
I also had connection problem(now it is solved)
and I suspected the collision of drivers.
So I connect pixhawk and apm and go to control panel and removed its driver
and deleted mission planner and reinstalled mission planner and dont connect other device excepts pixhawk 2.1
and make sure you have to upload firmware before you press connect button on the mission planner
and are there light on the pixhawk 2.1? its usb port is little bit loose so you have to use proper cable.
and along the setup, I turned off vaccine(sometimes kaspersky block some setup in background)
and.. do you still have this problem? not yet solved?