Pull codes and see what gives. A backfire upon deceleration or between shifts (esp if you back your foot off the gas while shifting, as many folks do during in-town driving), is a rich backfire. Extra gas is igniting in the exhaust.
During deceleration in gear, the puter will dial back injector pulsewidth and make a few other mods (it actually is kind of involved in what all it does) to accomodate the high manifold vac (from the TB being closed and the low performance demand, yet the engine is still pumping).
Kris, HISSIN is right on when he says running rich could be a possibility. Mine would backfire every now and then during hard shifts. It was just unburnt fuel igniting later on. But definitely pull the codes. What kind of mods do you have? o/r mid-pipe? afpr?