What exactly happens on the over-run? Is it backfiring? And what pipe are you running? If aftermarket, does it have a dB killer installed?
They will all tend to backfire a bit on the over-run. The stock mufffler tends to mask it pretty well and the sound of it becomes both more noticeable and more prevalent the more 'Open' the pipe.
It is one of the peculiarities of the Webber system that the ecu will keep delivering the idle fuel, that which is delivered at 4.8* throttle angle in the case of a Stelvio, at all engine speeds when the throttle is closed. Now while the crank is turning at idle speed the fuel delivered is just sufficient to keep the afr correct-ish so the engine will run and the mixture will ignite every second revolution as it should.
The problem occurs when the motor is spinning harder and therefore pumping harder. As the engine slows down the rapidly pumping pistons will greatly increase the manifold depression on the engine side of the butterflies so more aiir gets pushed past them. Now the ecu is delivering just enough fuel for the engine to idle but with this situation the mixture is incombustible lean. It won't ignite in the cylinder every revolution, it's simply too lean to do so and it gets pumped through the motor and expelled unburnt into the exhaust. Over a period of cycles of the engine harmonics and residual mixture left behind as end gas in the cylinder will periodically reach the point where the mixture will ignite and when this happens as soon as the hot, still burning, exhaust gasses are expelled into the exhaust they will ignite the previously expelled unburnt mixture causing the backfire. Harmonics play a big part in this and you will probably notice that the backfiring will occur at certain precise points as the engine is slowing down. That's why.
Most fuel systems nowadays get around this problem very easily. They simply stop all fuel delivery on a closed throttle until the engine slows down to a certain point. Phil has previously explained that it is very easy to do the same thing with the Webber system. You just yank the map out of the ecu, open it with Tunerpro and then reduce all the figures in the first two columns of the map to zeroes above the point where you want fuel delivery to recommence. Most people who do this opt for 2,500-2,700 rpm. It has the added advantages of slightly increasing engine braking, reducing fuel use as well as killing exhaust popping stone dead! If there is no fuel being delivered then there is nothing to burn. Nothing to burn and there is no backfiring! Simples!
Also if you are an easily entertained peasant like me it means that on hills like the one descending into Queanbeyan from Bungendore you can go down the hill in a high gear using engine braking to slow you down and playa game where you judge your slowing down so when the fuel cuts back in and causes the bike to give a little lurch as it does so it coincides with passing the 60kph speed limit sign on the edge of town!
Yeah. I'm a bear of very little brain....