It shouldn't.
Once started you are making electricity with your alternator and theoretically, you could even disconnect the battery and run without.
I say theoretically because some auto engines like Jeep, monitor +12V off the battery in the PCM as opposed to most who monitor it off the alternator.
Odd that you say it goes away. Almost sounds more like an air bubble in the fuel line, but yeah, if its under warranty, get it looked at.
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