I have cleared the whole configuration for the Flirc each time I have tried before setting the whole thing up again and I have also now tried with the Interkey setting in the Flirc Software at every setting from 0-6 and none fix the problem!
I can upload a video but it is not really going to tell you much more then what I have described: When I press the Prev button on my Harmony remote in something like XBMC which is set to the Back button on the FireTV config in Flirc it sends the command twice most of the time so instead of backing up one screen it backs up 2 screens!
Showing you this on a video will just be exactly as I described in words.
The next thing I will try is to map the Back button to a different key on the Harmony remote (Maybe the Menu button) and see what results come in for that, this does though point to an issue with the Flirc as I have had this Remote for years and it currently controls 8 devices and not once before have I had an issue with it sending a command twice to any device besides the Flirc...