Hi Guys
Thanks for the replies.
@DuaneB: I would like to integrate a joystick with my remote control transmitter using just two channels via the trainer port.
@AWOL: I have made the changes you have suggested (see below). I have also added a synchronisation pulse. Still not working.

Cheers
Jase
//PPM Signal Test 1
int startFrame = 0;
void setup(){
pinMode(13, OUTPUT);
}
void loop(){
startFrame = micros();
//Channels 1 & 2
for (int x = 0; x < 1; x++){
digitalWrite(13, LOW);
delayMicroseconds(400);
digitalWrite(13, HIGH);
delayMicroseconds(600);
}
//Channel 3 (Should run motor at full speed)
digitalWrite(13, LOW);
delayMicroseconds(400);
digitalWrite(13, HIGH);
delayMicroseconds(1600);
//Channels 4, 5 & 6
for (int x = 0; x < 2; x++){
digitalWrite(13, LOW);
delayMicroseconds(400);
digitalWrite(13, HIGH);
delayMicroseconds(600);
}
//Sync pulse
digitalWrite(13, LOW);
delayMicroseconds(400);
digitalWrite(13, HIGH);
//Wait until frame of 20000 microseconds has passed
while (micros() - startFrame < 20000){
delayMicroseconds(1000);
}
}