This is a snippet from another site:
"Extremely Lean fuel mixtures burn slower because the fuel molecules are farther apart & if the the fuel hasnt all burned off by the time the intake valve opens again, the incoming charge will be ignited and blow back out the intake."
I'm combining that with my personal experience to hypothesize that you are loosing fuel pressure when the ignition is off. Possibly the Mast cam allows valves to open longer / wider / sooner to make the engine more prone to it.
On my buggy once I shut the pump off I can watch on my fuel gauge as my fuel pressure drops, it will go down to about 20-40 psi and hover there for a while. If it sits for a few hours it will eventually drop to zero. I have no clue where it is going because I have no leaks, I have checked all the injectors, and I have check valves after the fuel pumps. If I start my buggy at these lower pressures it will run rough for a second until pressure builds up again. It will be perfectly fine until it sits for a while again. My LS2 doesn't backfire though, possibly because I have a stock cam. Maybe GM was aware of this and designed their cams to prevent it? Or maybe Mast just pushed the envelope a little too far and doesn't want to recall a batch of cams?
In factory form the fuel pumps have built in check valves to minimize the loss of pressure. But even they aren't perfect which is why the ECM primes the pump for 3 seconds the instant you turn the key. If my rig has sat for a really long time that 3 seconds is rarely long enough to fully prime the system up to 60 psi. I have a manual pump button in my cab that I often use to finish priming.
So long story short, your have low fuel pressure during the initial start, lean condition occurs, takes longer to burn, and continues burning after the intake valve opens.
I've heard a backfire can destroy the plastic intakes. I would want this fixed, especially if you have a $1000 FAST intake.