not sure - perhaps there is a warm-up period tied to engine temp which takes about 30 mins to get to? you mention the problem on restarts - cold starts also?
really, once someone has been in messing w the ecu then all bets are off. the fact that you are running a 987 maf holder means they have done some black kung-fu in there, as others have been told by them that you cant change the maf conversion map (in a 7.2, anyways; perhaps more flex in a 5.2.2?).
can't think of what else works on a timer to make it screw up at exactly 30 minute - secondary air system perhaps?
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