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Going off what everyone else has already said, never, EVER, tune your vehicle under warranty. The ECU is responsible for so many things on the car that it's easy for the dealership to say that a tune is responsible for any engine, exhaust, intake, and electrical issue.
Some dealerships will view tampering with the ECU at all as a warranty void. I've heard of multiple ways that they can check to see if a tune has been flashed, even if the owner flashed the stock setup back on the car. The most plausible method I've heard of is that they can see a log of all the times the ignition has been activated, so if you've had the car for over a year or so and it only has 2 ignition starts logged then they pretty much know the ECU was flashed.
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