Safety issues

The Throttle Cut switch is intended to be used for shutting off the engine to prevent inadvertent operation of the throttle stick. When this switch is closed, the throttle control stick is disabled.
You should always close the Throttle Cut switch before turning on your transmitter. Open the switch only when you are ready to operate your RC model and at a safe distance from it.

The software checks the position of the throttle stick at startup when you turn on your transmitter, and each time you exit the Command mode.
If the stick is not in the idle position, it will be disabled. The buzzer and the LED will play the Throttle alarm code and the engine won't start.
To re-enable the stick, move it down to the idle position. This will resume normal throttle stick operation.

Setting the throttle security threshold: usually, the throttle channel potentiometer does not provide exactly zero Ohms at the idle position. The threshold value checked by the software is defined by the Global variable TSC. If the buzzer and the LED keep playing the Throttle alarm code the first time you use the software, then your throttle potentiometer idle position is probably over the TSC value: follow the Throttle calibration procedure to change TSC.

If the receiver is already turned on when you power-on the transmitter, then the receiver may send unwanted signals to the ESC and other servos for a short time, leading to an unexpected and dangerous engine startup. This issue has been observed with the "GT-2 2.4Ghz 3Ch" and "2.4Ghz 6Ch V2" receivers from Hobby King.
You should always turn off the receiver before powering on the transmitter, and then wait 2 seconds before turning on the receiver.

This behaviour is caused by the Arduino bootloader: when the transmitter is turned on, the RF module starts shortly but it takes a few seconds for the Arduino to start the transmitter program because it executes the bootloader(1) first. During this short delay, the RF module is out of control. This hazard could be avoided by uploading the transmitter software with an external programmer, therefore eliminating the bootloader.

(1) bootloader: a small program that has been loaded on to the microcontroller on your board. It allows you to upload code without using any additional hardware. The bootloader is active for a few seconds when the board resets; then it starts whichever sketch was most recently uploaded to the microcontroller. The bootloader will blink the on-board (pin 13) LED when it starts (i.e. when the board resets).