Finally i found the problem.
I had activated gpio controllers, and when the n64 emulator starts, assigned the gpio 1 and 2 to 1 and player 2, and the sixaxis was the player 3.
I solved configuring gpio to 0 in recalbox.conf and It works fine.

Thanks for all.

@Substring nop...I only have the sixaxis bluetooth conection. and when the n64 starts, the player 4 led stay on

@Substring no way.... After reconfigure in ES.. continue as before...

My sixaxis ps3 controller don't work when the n64 emulator start.
It only happen when i'm using bluetooth conexión.
But i can back to the front with hotkey...
If the sixaxis are wired conect there is no problem.
And the leds stop blinking and stay turned on the led 4.