Arduino micro timer 1/3 synchronisation

Hello,

I'm trying to synchronise arduino micro (32u4) timers 1 and 3.
Both those timers are used in CTC mode, toggle output on compare.

I first made this code :

            // Enable CTC mode, timers stopped
            TCCR1A = 0x40;
            TCCR1B = 0x08;
            TCCR3A = 0x40;     
            TCCR3B = 0x08; 
            
            // Set phase 
            TCNT1 = TCNT_value;
            TCNT3 = 0;
            
            // Set frequency
            OCR1A = OCR1A_value;
            OCR3A = OCR3A_value;

            if((PINB&0x20)!=00) TCCR1C=0x80;
            if((PINC&0x40)!=00) TCCR3C=0x80;
            if(TCNT_value == OCR1A_value) 
            {
              TCCR3C=0x80;
              TCNT1 = 0;
            }
          
            // Start timers
            
            bitWrite(TCCR1B, CS10, 1);
            bitWrite(TCCR3B, CS30, 1);

But I noted a delay of approximately 0.99 µs when I input a null phase ( TCNT = 0 ).
Then I read a bit on the internet and of course the atmega32u4 user manual and tried to use GTCCR, which resulted in following code :

            // Enable CTC mode, timer stopped
            TCCR1A = 0x40;
            TCCR1B = 0x09;
            TCCR3A = 0x40;     
            TCCR3B = 0x09; 

            GTCCR = 0x83;
            
            // Set phase 
            TCNT1 = TCNT_value;
            TCNT3 = 0;
            
            // Set frequency
            OCR1A = OCR1A_value;
            OCR3A = OCR3A_value;

            if((PINB&0x20)!=00) TCCR1C=0x80;
            if((PINC&0x40)!=00) TCCR3C=0x80;
            if(TCNT_value == OCR1A_value) 
            {
              TCCR3C=0x80;
              TCNT1 = 0;
            }
          
            // Start timers 

            GTCCR = 0;

And again, ~ 1µs delay as you can see on that logic analyser picture :

http://hpics.li/1d749c2

I'm using frequency of ~ 8-12 khz. 1 µs is a quite significant phase offset at 12 khz.
Do anyone have an idea of why timers 1 and 3 are not synchronising ?

King regards
Aurélien