Go into your settings and change the fuel mixture on decel to stop the popping. FP3's offer that ability to change many things. Had the same issue you did, click of my finger and it was solved. Don't fault the tuner if you don't use it to the fullest advantage that it offers.

 

Let us know how this plays out, I had an FP3 on my Superglide and after a few long rides and applying the autotune changes the bike ran great, no more decel pop and mileage was great. I bought my current bike and there was a TTS in the tourpak and the dealer I bought it from couldn't get the tune right and I am still trying to learn it so I can get it right. Research the guy doing the tuning because the dealer put mine on a Dyno 3 times and it never was right. Found a guy 170 miles away that is pretty good with the TTS so a little better now.