First off, this is a great device, love it paired with the Flirc USB. My setup is as follows: OdroidN2 with Flirc, Sony TV, AppleTV. I have the A program controlling TV and Apple TV. The B program controlling TV (to turn on) and the OdroidN2 with Kodi, and the C program controls just the TV.

When I am viewing Kodi, with the remote on the B program, everything works fine. But, when I switch the remote to C and control the TV to change input or do something related to TV specific functions, it still controls Kodi and the Flirc at the same time in the background, causing Kodi to go through settings or play something or whatever.

Is there a way to prevent the TV buttons from controlling the Flirc at the same time?

I have exactly this problem and am hoping for a solution. The tv commands control kodi and flirc even when I am in a program that does not include flirc/kodi (equivalent of your program C).