The issue comes down to how the device interacts with your computer. Just like the original version, the new Steam Controller has no native Windows drivers. This means the hardware relies entirely on the Steam app to function properly. If you do not have the game running via Valve’s storefront app, your shiny new gamepad turns into a useless piece of plastic.
Gamers Nexus also reported this and there are a lot of other news outlets also covering this. It is kinda the same as with the steam deck where I noticed that the inputs just don’t work until steam is launched. I really don’t like that I have to have Steam running for this controller to work. I don’t know if it is a dealbreaker for me, yet, but it really put a damper on my enthusiasm about it
I already launch most controller-based non-Steam games I own through the “add a non-Steam game to Steam” feature because Steam Input is the best game controller driver/manager I’ve used and it’s not remotely close.