MultiWii

with tricopter there is esc signal in pins: 2,3, 5,6

i think pin 2 is disable with tricopter

with clean code only set TRI and GY_85

NUMBER_MOTOR is 3

#if defined(MEGA)
#if (NUMBER_MOTOR > 0)
// init 16bit timer 3
TCCR3A |= (1<<WGM31); // phase correct mode
TCCR3A &= ~(1<<WGM30);
TCCR3B |= (1<<WGM33);
TCCR3B &= ~(1<<CS31); // no prescaler
ICR3 |= 0x3FFF; // TOP to 16383;

TCCR3A |= _BV(COM3C1); // connect pin 3 to timer 3 channel C
#endif
#if (NUMBER_MOTOR > 1)
TCCR3A |= _BV(COM3A1); // connect pin 5 to timer 3 channel A
#endif
#if (NUMBER_MOTOR > 2)
// init 16bit timer 4
TCCR4A |= (1<<WGM41); // phase correct mode
TCCR4A &= ~(1<<WGM40);
TCCR4B |= (1<<WGM43);
TCCR4B &= ~(1<<CS41); // no prescaler
ICR4 |= 0x3FFF; // TOP to 16383;

TCCR4A |= _BV(COM4A1); // connect pin 6 to timer 4 channel A
#endif
#if (NUMBER_MOTOR > 3)
TCCR3A |= _BV(COM3B1); // connect pin 2 to timer 3 channel B
#endif

there is same problem?

resolved with this and pin 2 remain high without timer signal

#if defined(MEGA)
#if (NUMBER_MOTOR > 0)
// init 16bit timer 3
TCCR3A |= (1<<WGM31); // phase correct mode
TCCR3A &= ~(1<<WGM30);
TCCR3B |= (1<<WGM33);
TCCR3B &= ~(1<<CS31); // no prescaler
ICR3 |= 0x3FFF; // TOP to 16383;

TCCR3A |= _BV(COM3C1); // connect pin 3 to timer 3 channel C

digitalWrite(2, HIGH);

#endif
#if (NUMBER_MOTOR > 1)
TCCR3A |= _BV(COM3A1); // connect pin 5 to timer 3 channel A
#endif
#if (NUMBER_MOTOR > 2)
// init 16bit timer 4
TCCR4A |= (1<<WGM41); // phase correct mode
TCCR4A &= ~(1<<WGM40);
TCCR4B |= (1<<WGM43);
TCCR4B &= ~(1<<CS41); // no prescaler
ICR4 |= 0x3FFF; // TOP to 16383;

TCCR4A |= _BV(COM4A1); // connect pin 6 to timer 4 channel A
#endif
#if (NUMBER_MOTOR > 3)
TCCR3A |= _BV(COM3B1); // connect pin 2 to timer 3 channel B
#endif

Can you explain what your goal is? It's not clear. The 4th signal in tricopter mode is for the tilt servo.