Since it's a new bike, it's entirely possible the tire wasn't seated properly in the rim. Things like what happened to you are most likely to occur at the beginning of a bike's service life; it's part of "shaking the bugs out". The LBS should put this right as part of the warranty service.
And once you realize how much more reliable and easier to pump they are, you'll grow to prefer "those little presta things".
Enjoy the new bike.