Help me De-Bug: X-Box One Controller Issues?

Interesting problem, folks. My aging but still solid battle-station started behaving weirdly after entering FPS games over the past few days. Noticeable delay on audio on load, and then video failure while audio was solid in-game. Additionally, my rig didn't seem to respond to keyboard or mouse commands despite no drop in audio feed.

My first thought was that my aging GPU was giving up the ghost, so I stress-tested (fine) and then updated the drivers. Problem continued.

Next thought was failing ram, so I tested for that; all green.

Next thought was that my storage HD was failing, so I checked for errors and listened during operation; all okay there.

Next thought was that my games may have corrupted files somehow, so I tested by deleting one of the games that were messing up and re-installing. The game continued to have the same issues after this treatment.

Finally, I decided to check the USB connections on my keyboard, mouse, and controller (X-Box One Mini Controller). I disconnected them one at a time and opened up the game to see if a manual connection was causing the problem. No change with mouse or keyboard being disconnected, but with the controller disconnected all problems went away.

Question for the audience: has anyone else run into this issue before? I only recently got a controller so I could play some fighting games on steam, and I don't use them for FPS. Not having the controller connected most of the time is therefore not an issue for me, but I'd like to not have to remember to unplug it if I want to play something else. Any solutions?