Unfortunately, most of TLS's controller support is just hoping the underlying engine does its job right, which it sometimes doesn't. On that note, are you quite certain it's undetected rather than just being configured weirdly? You might try switching around the buttons in the confusing F1 menu.
You also might try a program like Antimicro that lets you emulate keyboard inputs with your controller. This is an approach worth trying in general for games that don't support controllers or don't recognize your particular controller. Just the other day I heard of someone using this approach for Desecration of Wings.
Steam version is RTP version but I strongly doubt that matters.