From Our Friends at DynoJet
Popping on deceleration is due to unburnt fuel being ignited in the exhaust. The reason you do not hear this on a bike with a stock exhaust is due to the baffling of the stock exhaust. It is not only much quieter but also does not allow the fresh air to enter the exhaust due to reversion. This fresh air makes the exhaust hotter (think of letting a fire have more oxygen) which aids in the combustion of the unburnt fuel.
To REDUCE (it may not totally go away) popping on deceleration first make sure that you do not have any intake or exhaust leaks. If all that checks out then you can alter the fuel curve at closed throttle to help this problem. If you are using a PCIII then go into the 0% column of the software and alter the fuel curve from 1750-5500rpm. The value you enter depends on your model and setup. Some Magnetti Marelli bikes responded by having a -60 put in this column while most Delphi bikes respond by inputting a +25. Also make sure that you synch the Throttle Position so that it reads 0 while the bike is idling.
Wrench Safe, FMH