I"m using FLIRC SE, with a linux-based Kodi HTPC build (mini ITX fanless etc). This build has been working great for a year now.
The FLIRC SE is only connected to USB - without the connection to the Power Supply, as I only need it to wake the HTPC from "suspend to RAM" (S3) state, I don't need it to wake the HTPC from S5.
The remote is a Harmony Hub with the simple RF remote (they call it Harmony Companion these days). I use it to control the HTPC (Kodi), the Smart TV and my Receiver