hoahai-The manual you posted is different than the 2008 manual that came with my car.
On page 2-16 of my manual it says "if the battery on your vehicle has been recharged, disconnected, or is not working, you will need to reprogram the driver's power window for the express-up feature to work. To program the driver's window, follow these steps:
1. With the ignition in ACC/ACCESSORY, ON/RUN or when Retained Accessory Power is active, close all doors.
2. Press and hold the power window switch until the window is fully open.
3. Pull the power window switch up until the window if fully closed.
4. Continue holding the switch up for approximately two seconds after the window is completely closed.
The window is now reprogrammed."
I just noticed that the manual online is for the Malibu Classic so that may be the difference.