A deep note and some shake 2001lxi please help!!!

My car, a 2001 lxi is rarely driven, just got 5k miles on it since it was brand new. The car is just great,and a good package for the buck too. However, the car seems to have a slight shuddering under you feet when your accelerating that usually comes with a low whining/grinding noise that pitches up when you accelerate further. i took the car to the dealer (still under warranty) and told them about the problem and that the noise was never existed the first four thousand miles. They lifted the car done a full computer/ visual check, and told me that the car is perfectly well, and no need to bother about it. again i know what i'a, hearing, its just that this damp somehow irritating sound wasn't there to start with, plus, the car is in a dealer condition. Please anyone help?