To start this topic, all non Steam games I have I link to Steam using the Add a non Steam game function.

Yesterday I noticed with my copy of Witcher 3 (GoG) the controller wasn't working. No matter what I did it wouldn't work. I then started the game from the .exe and the controller worked. Go back to the Steam shortcut, controller does not work.

This morning I decided to fire up Assassin's Creed (GoG). I haven't played it in a long time, but my memory says I used the Steam shortcut and the controller worked fine. Today, it doesn't work.

My entire run of Far Cry 4 (and 3) was used through Steam shortcuts and I used the controller with both. Those games are currently uninstalled so I can't test. [EDIT: downloaded FC4, controller works] Same with other non Steam games I have. Has anyone encountered this? Any idea how to fix it?