Sorry for the long delay in reply. New baby in the house, hard to find time to mess with things. But, tonight was a night I could have a look at this again because it's now 5-10 minutes before the Shield will react to my harmony after a power on.
First, to answer some of jason's questions:
Using "FLIRC" manufacturer and "Kodi" device
Not sure by the question on what button is the harmony using to send a signal. I hit the "Watch TV" activity button. Looking at my activity list for "Watch TV", it actually doesn't show the shield in there, just my TV and Receiver. But, it eventually does work after 5-10 minutes of "warming up"
I'll get to this below (ruling out remote)
Unplugging the FLIRC and plugging it back in when it exhibits the issue after power on does not change anything
Couple of new things I learned:
After the 5-10 "warm up" period is over and the remote fully works. I can power off my system, and power it back up, and it works immediately. Not sure how long the remote needs to be inactive before it starts exhibiting the 5-10 warm up period again, it's a touch thing to test.
I borrowed a harmony hub from a friend (remote/hub) and set it up in my system continuing to use the FLIRC->Kodi device assignment, and it works fine without issue. So, to me, this rules out the FLIRC and points the finger completely at the Harmony 650 remote that I have. This was a quick borrow, so I no longer have it to test anything else out unfortunately.
So, it seems to be my Harmony 650 remote control. The remote has always worked fine in previous setups (using MCE USB dongle, Keyes IR GPIO for RaspberryPi, etc), and my TV and Receiver still react normally to the Harmony during this Shield "Warm up" period. I'm at a loss here.
I know this has now stretched beyond the FLIRC dongle, so I understand that support will be limited on this forum now, but perhaps someone can look at the above, and may know a simple answer.
Thank you for any help.