Can you describe the chatter a little more. I have an 05' 5EAT, and sometimes but not always, I get a chatter at around 2000 to 2500 RPMs under light load or throttle. Sounds like something is loose and rattling. But I can't tell if it's in the transmission, the engine, or what.
The engine was replaced last year, and the driver side CV axle at the same time. Just replaced the passenger side axle a few weeks ago. I first noticed the chatter around the same time. The passenger side axle was a new FEQ brand and was causing vibration at stops. Had that swapped for a remanufactured one. Vibration is gone, but the chatter remains.
So not sure if the chatter is associated with the tranny, engine, or that axle.