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I doubt it's a leak, but since the intake flows more air the MAF reading can be off. During cold idle when its not using the o2 sensors yet that can cause some cars to get a little choppy for the first 45 seconds until the car warms up and goes to closed loop mode.
I don't know if BM3 has adjustment for intakes built in or what but the table your tuner would change would rescale the MAF reading for the higher flow intake.
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