My controller stopped working in-game

I downloaded the Legendary Edition a few years ago and played the hell out of it using a Logitech F310 controller. A year or so ago, I set it down, and now that I've tried to start playing it again, the exact same controller has ceased to work in game. I don't think it's a problem with the controller itself, as it works 100% fine in other games and in the Legendary Edition launcher to select a game, but once any of the games in the series loads, it just stops receiving input from the controller. I've tried using different USB ports for the controller, re-launching the game, shutting down and rebooting my computer, and every controller configuration. Has anyone else had this problem before, and/or knows how to solve it?