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TLDR: launch the gog copy through Steam library to use keyboard/mouse and stop game alternating between keyboard and controller.

Problem Summary: Upon starting Syberia 3 the UI alternated between keyboard and controller with controller prompts flashing on and off and keyboard/mouse not working well. Even the title screen alternated between "press A" and "press Enter" every second or so.

Detailed description: I have three controllers on my PC - Sony style, N64 style, and a Nintendo Switch Pro controller; none of them seemed to get past the title screen with their "A" buttons (or "B", "X", etc). Using the mouse, going to the in-game options the image switched back and forth between keyboard and xbox controller (game provides no actual settings just an image of the input map). So, the game was clearly confused about what input to use. I tried playing with the mouse and keyboard, but flashing controller prompts were visually distracting and I was unable to complete the first puzzle (turn the screw on the call box with the knife) with the mouse - it was as if a phantom controller was fighting my mouse movements. So, I hit the internet in search of a solution and found many promising leads that didn't pan out. Changing the preferred controller in Windows settings didn't work. Physically removing all but one controller (the PS style since it seemed closest to xbox) didn't work. Running with Steam process exited and gog overlay accessible in game didn't help.

Solution: Eventually I tried launching the gog copy of the game through Steam by adding it to the steam library. I wanted to do this to access Steam's controller settings. For whatever reason, that seems to have convinced the game to use the keyboard/mouse without conflict and ignore the controller altogether. I've since reattached the other controllers and launching through Steam results in a playable keyboard/mouse setup while launching through gog with or without Steam running presents the buggy conflict on the title screen. So, while trying to get a controller working, I accidentally got the keyboard/mouse working instead. Good enough - I'll play with that combo instead. Hopefully that helps someone else experiencing that frustration. I'm fairly sure disconnecting all three controllers would also allow keyboard/mouse to work with gog, but that'd be a hassle to connect/disconnect them. Good luck! Have fun!