Mine vibrates in the same area. Only when the car is in gear and the clutch is out. It's smooth as silk until you hit the 3000-3200 rpm range on deceleration then you get the vibration.
I'm thinking it's a bearing problem in the clutch or drive shaft. I've never been in the clutch or drive system on the Boxster so I don't know if it has a "torque tube" like the 928 with more bearings. I'd imagine it doesn't since the engine is right on top of the transmission.
I'm going to pull the clutch some time in the next couple of months and see if any bearings have play in them. I'll probably go ahead and just replace the pilot and release bearings while it's open and check the RMS. I'll post what I find when I get around to actually doing it.
