I'm having the same problem here now. Was using XBMC 13.2 and did not have the issue (or had it resolved there at least), but upgraded recently to Kodi 17.3 and the problem (re)occurred. I'm using a Harmony One remote set to emulate a Syabas PopcornHour C-200 device. Target computer is a Win 7 HomePremium laptop. Flirc firmware is 3.6.
Noise-Canceller is turned off, Inter-Key delay is set to 2, built-in profiles are enabled, sequence modifiers are disabled.
Let me know if there is any more information I can provide to assist with resolving the problem.
my_flirc_config.fcfg