It's all good. Since I knew it worked before I upgraded firmware (although it could be any combination of Logitech stuff, etc.) I basically nuked everything from the Flirc install, Harmony install, as well as all the programmed remote settings.
I reinstalled everything, upgraded all the firmware, updated all logitech software, and then re-customized remotes/activities. All good now! Thanks! I didn't want to spend time debugging each element to figure out what broke what! It's back to normal now. Thanks again!