If you are using steam and an Xbox 360/Elite Controller, try the following:
In steam, right-click Warframe->Properties
At the bottom of the General tab, change the Steam Per-Game Input Setting to "Forced Off"
It disables DE's "controller mode" integration with Steam and set things back to how there were before whatever update that was back whenever. I've just tested this now, after I downloaded the update and I haven't had any controller issues so far. Everything is working as it should be. If you need to rebind, you can use the Xbox Accessories app from the desktop in Windows 10.
Not sure how doing this will affect a Steam controller, but it should work with a PS4 controller as well.