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I never found this in Googling, so thought I would save someone frustration. I had been trying to use my Steam controller with GOG version of Alan Wake. But upon starting Alan Wake, got a UAC popup (Windows 10) and from then on the controller was unresponsive. I tried disabling UAC, that also had no effect. So then I added it to Steam as a non-Steam game... no luck. The way I fixed it was I changed the security settings on the alan_wakes_american_nightmare.exe for Users (*\Users) so that Full control was given. This took care of it. Maybe this will help with other GOG games.
Post edited September 24, 2017 by vladikus