Why isn't my controller working when launching as modded?
If the game opens a terminal window when launched as modded, there's a high chance that terminal window is consuming the controller input and the game never receives them.
In order to get the controller working again, you should look for a way to disable the terminal window. The methods for doing so vary depending on the mod loader used, here are instructions for the known ones:
In games where BepInEx is used as the mod loader, the terminal window can be disabled by editing the BepInEx core config as shown below:
Note Remember to save the settings!
Note If you have no configs, make sure to launch the game as modded at least once after installing BepInEx. Configs are generated on launch.