5 speed; whining in third

My wife's 2002 X whines loudly in third gear. This is the only manual X I have ever driven so I have nothing to compare it against. Does anyone else's do this? It just turned 1000 miles and the noise is unchanged. Maybe it needs a break-in period?

Where does the whine come from? Front or Rear? What RPM's? Does the whine change or go away when you depress the clutch?

The truck is brand new have you had the dealer listen to it?

The sound is coming directly from the tranny, it is most pronounced to the passenger in the vehicle. It is starts as soon as the clutch is let out in third, and the pitch changes as the speed increases. I have not yet been back to the dealer about it, I first wanted to see if anyone else had this problem.
I am myself a "Land Cruiser guy" and I know that some trannies are just loud, I thought maybe this is one of them. It's looking like I'm the only one having this problem, so I guess my next step is the dealer.
Thanks,

Also the noise does go away when the clutch is depressed, making me think it is an internal tranny noise.