Call flowmaster...
Edit
Spoke with flowmaster,
"our mufflers cannot burn in, the only reason the sound would change is if a baffle blew out or the muffler rusted out. If the tone changed with our mufflers on the car some thing else changed. Like a converter getting more or less plugged or melted, a resignator getting worn or the tune changing". Call for your self if you don't believe me. No hard feelings just stating the truth from the manufacturer!