ArduPilot Mega: 1000-2000 usecond range for Servo

running 4 servos with ardupilot mega board, using the code below, i get a little jitter...can any1 help to see if i am doing any mistake?...
i am running Ardupilot Mega (atmega1280) on 16MHz...

TCCR1A =((1<<WGM11)|(1<<COM1B1)|(1<<COM1C1));
TCCR1B = (1<<WGM13)|(1<<WGM12)|(1<<CS11);
OCR1B = 3000; //PB6, OUT2
OCR1C = 3000; //PB7 OUT3
ICR1 = 40000; //50hz freq...

TCCR5A =((1<<WGM51)|(1<<COM5B1)|(1<<COM5C1));
TCCR5B = (1<<WGM53)|(1<<WGM52)|(1<<CS51);
OCR5B = 3000; //PL4, OUT0
OCR5C = 3000; //PL5, OUT1
ICR5 = 40000; //50hz freq

How much is "a little"? What is the rest of the program doing?

i am working on a different approach for a quadcopter...
i am using a r/c transmitter to control the servo....the rest of the program is controlling the servo with the gyro reading...

its a kind of constant jitter....like 4-5 times in a second if i move the servo slowly with the transmitter....it only happens when i try to control the servo with the transmitter....with gyro movement, the servo works fine.

any help at all?....

I have not piped in until now because I was worried about admitting that I do not recognize the code snipped you posted as servo communication. But I will admit it. I do not see servo code in what you posted.

I am sure that there are other ways to do it, but I am used to seeing the servo library used to communicate with servos.

i am using a r/c transmitter to control the servo....the rest of the program is controlling the servo with the gyro reading...

So, you want to read in the output from an RC Receiver, and read in the output of a gyro. Good. I assume that you will then perform math on the various inputs to determine what outputs should be sent to each motor. Good.
If this is not an accurate overview of what you want to do, say so. It will help us if we have a better understanding.

You mention servo jitter. I assume that you are using servos but will eventually use RC hobby ESCs. How are your servos powered?

i have fixed the problem....
the timer function was correct....i had a read delay from transmitter set in the software....after reducing it, everything is the way i wanted it to be.

Thanks.