Is the "backfire" coming out the exhaust or the intake? A check of the intake area (burnt/singed aircleaner or blown off hoses/tubes/etc) could yield some clues.
In the old days back-firing through the intake was usually a sign of bad valve/ignition timing or a lean condition.
Granted, the new cars are now heavily loaded with elec. gadgets, but the fundamentals are still the same. Either the timing chain has a mind of its own (not the case if it has spells of running "normal") or It thinks the plugs need to fire earlier than they should, or something is making it run lean.
Those are my two cents...I am curious to see what others think.
"...rationality of thought imposes a limit on a person's concept of his relation to the cosmos." -Nash
04/71 280SE 195k
09 Jetta TDI