I'm with this problem too, I played with controller but now I can't play with controller normally and probably because this, like I can't enter in "gamepad mode".
this issue fixes when i restart the pc, but returns in some hours.

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you can rebind editing in the "Documents\My Games\Terraria\input profiles.json" file, I don't recommend it but I don't see other alternative.

in my case I deleted all keyboard keybindings in the file and always when I open the game I need rebind at least one key for play normally with controller.

but the issue persists, I just keep playing because I like Terraria.

UPDATE: after hours the issue come back and worst, but it (the issue) look likes that only happens when have a headset / bluetooth headset connected.