hmmmm...i never used the dock...but i still use the first gen's usb cable to connect to my 3G..and that works fine. I dont want to tell you that you might messed up the pins...why dont you try to use just the usb cable and connect to your 3G see if that will work? Nevetheless, i think you can return it at Apple and get a new one for that reason...Just be sure it's in the factory settings. Good Luck.
Seems to be the case for most iPhone (car) accessories as well. If I were to guess, I'd say that they jumbled around the pins to serve different purposes.
the 2G dock works just fine with the 3G phone. I'd recommend you use canned air or your face to blow the fine white plastic particles out of the dock, also check your phone in case some of the plastic bits got lodged in the port. I found dremelling out the dock to be quite messy, but with some canned air I was able to clean it out and it works just fine.