My 3DS actually started making the noise I believe you are describing in the op when pressing down on the a button. I started noticing it when I was playing either Super Mario Land 1 + 2 from the VC. When holding down the run button and then hitting the jump button was when I first started hearing it. It almost sounds like it needs some lube or WD40 on the buttons. I won't do anything yet to it and it seems like it is only the Mario VC games that I notice it so far (I haven't played that much Super Mario 3D Land) again since getting MK7. Anyways, this noise is kind of pissing me off too but I am not sure what to do about it yet (since it is not happening that often I kind of put it on the back burner for now).
Anyways, I would probably just go through Nintendo unless the store is willing to replace it again. Reminds me when I first bought the DS phat. I took it out and noticed the bottom touch screen was dented on one side. I then tried to see if it still worked and of course the touch screen was screwed up. I took it back to Gamestop while on the phone with a Nintendo rep (lived across the street from Gamestop) so the Nintendo rep could talk to the employee. I suppose they believed me and the story (I sent the receipt back to them to show that on the same day purchased was when I called to report). I sent in the DS free shipping and they sent me another one free of charge. The employee at the Gamestop was like good thing you didn't purchase our protection plan because you would have used it up on the first day. So basically I could have purchased a protection plan (probably 15 or so dollars) and had to use it right away due to getting a damaged system out of the box. I would then have to repurchase another plan for the new. That is when it is better off to call Nintendo.
