We've changed the channel that reads the throttle on basic ArduPilot from pin 13 to pin 11. That's because pin 13 shares an LED, and it's causing problems with some low-voltage RC receivers. Pin 11 is clean.
The above picture shows the correct jumper wire configuration. If you've been using pin 13, please switch it to pin 11.
In the code, you tell ArduPilot which pin you're using with this line:
#define THROTTLE_PIN 11 // pin 13, or pin 11 only (13 was old default, 11 is a better choice for most people)
Sorry about this messiness, but it's all in the service of extracting as much utility as possible out of the basic ArduPilot board (which was originally designed not to control the throttle at all--those were simpler days!). Later this year we'll release a new version of the ArduPilot board which will clean up everything nicely (same features, so nobody will be left behind), but for now, please whip out your soldering iron and switch the jumper.
The manual has been updated with the new instructions.