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I have this very same problem. I am running Flirc on Windows 7 pro with a Logitech Harmony 350 remote. I can see in the GUI Flirc is connected and says its recording keys. But outside of the GUI the remote does nothing at all. I have confirmed the Flirc and remote work fine on my Mac computer with the default Kodi profiles. I have tried reinstalling, reprogramming remote, Zadig driver install, but nothing is getting it to work on my Windows HTPC.