[TheOtherGuy]

Originally Posted by billbo911

Without seeing your code I'll have to take a SWAG. It sounds like the transmitter is in 23 mode. Try switching it to 12 mode.

I tested that just now and instead of replacing 2 for 3, it caused channel 1 to move all 4 motors.
Here is the code:

#include "UserAPI.h"

int motor1;
int motor2;
int motor3;
int motor4;
int ch1;
int ch2;

void main ( void )
{
    while ( 1 )
    {    
        ch1 = GetRxInput ( 1 , 1 ); //get input from channel 1
        ch2 = GetRxInput ( 1 , 2 ); //get input from channel 2
        motor1 = 255-ch2; //set motor1 opposite from motor2
        motor2 = ch2;
        motor3 = 255-ch1; //set motor3 opposite from motor4
        motor4 = ch1;
        SetPWM ( 1 , motor1 ); 
        SetPWM ( 2 , motor2 );
        SetPWM ( 3 , motor3 );
        SetPWM ( 4 , motor4 );
    }
}

It works just fine with the second transmitter and the configurations are the same on both transmitters.