Page 105 of the 2003 manual states:
"If your vehicle's battery is disconnected or goes dead, or the driver's window fuse is removed, the AUTO function will be disabled. The power window system needs to be reset after reconnecting the battery or installing the fuse. You should do the following.
1. Start the engine. Push down on the driver's window switch until the window is fully open.
2. Pull back on the driver's window switch to close the window completely, then hold the switch for a second or two more.
If the power windows do not operate properly after resetting, have your vehicle checked by a Honda dealer."