Aye Steve,
Air leak into the exhaust system at the join between the silencer and exhaust pipe. Sucking air (oxygen) in on the overun/closed throttle causing unburnt fuel to ignite in the silencer. Change of back pressure may also initially confuse the EFI. Use some exhaust assembly paste to ensure a good seal if you haven't done so already. If a leak still persists, then a sleeve manufactured from a tin can, exhaust assembly paste and the use of a jubilee clamp, instead of an exhaust clamp might help. Exhaust clamps do not always give a 360 degree all round pressure on the joint and can allow a leak through the expansion slit/s on the silencer, if they align with the gap in the exhaust clamp.
However, this may be all *****

as I have never had to deal with EFI's!

I am sure that the sage's will be along to give chapter and verse on 'Thunder Guts'.

Regards, Bill