I am using the Flirc SE edition with firmware 3.7 (for some reason it will not get updated to 3.8 no matter what I do). The remote I have programmed is Harmony 650 with the Kodi/Flirc device. In the Flirc software I have mapped my keys to the Kodi layout. I recorded the power command via flirc_util (I used the power command from a WD TV Live that I learned into my Harmony).

My issue is that most times the Flirc will not properly turn on the PC from complete shut down. The PC will try to start, the power LED will flash for half a second and then the PC will not start. The second press of the power button on the remote starts the PC normally. Also the same button shuts down the PC normally every time. Using the Help button on the Harmony does not alleviate the problem.

I tried re-learning all command into the harmony and flirc a couple of times and nothing helped. My hardware power button shuts down and turns on the PC normally every time.

I am excluding hardware wiring error, and motherboard setup error because the Flirc will work on the second attempt.

Does anyone have ideas what can I do?

Are you sure that this is not a problem with the motherboard itself? Are you experiencing the same problem when using hardware power button?

If this doesn't happen with the hardware button then maybe you get double press from the remote and the PC simply turns off when it receives the signal again.