During setup one of the controllers never showed in headset or on computer, yet its status light on the controller was green. Charging it now, showing orange. Even on Steam VR it is not lit up. Do we follow the pair controller choice?
@Koda6786, this type of stuff is often related to USB compatibility. Try switching USB ports on your PC. In many cases, I tend to trust the indicator light on the controller/basestation more than SteamVR's indicators however, SteamVR does tend to be accurate after 30 seconds to a minute. The real test is weither or not both controllers are actually usable. If not, there are a few troubleshooting steps you can look towards. There is a helpful "unpair all" procedure that often helps that I'll PM you.
I'm developing a game for the Vive, if you're using VRTK it makes the controllers disappear in unity 5.6 (latest supported version is 5.5.3) when I moved back to the old unity version everything went back to normal I hope this helps ..