The wheel is balanced, but when you install that wheel onto an assembly the assembly is not balanced. Every one I have had on the machine has needed some balancing. If the wheel is a cast one, then it usually needs more work. If the wheel was machine from a billet they are usually much better out of the box.
Just because the turbo was balanced does not mean once you disturbed it that it will automatically be in balance when the new wheel is installed. When you install the new wheel onto the shaft you run it on the balance machine and then, depending on what the machine tells you, you make rotational changes using the notch machined into the wheel at the factory.
Garett says that any time the turbo is disassembled the following components need to be checked for balance (the compressor and turbine wheels are checked individually at the MFG): 1) Turbine wheel and shaft 2)thrust collar, 3) oil slinger, 4) Compressor wheel, 5) nut. Holset and BG also have similar requirements when working on their turbo's.