Read both the camera and flash manuals - in detail. suggest you look in detail at the flash, redeye reduction and AF sections. there are various settings that may override one another. I have managed to successfully suppress the AF assist lamp in the settings banks where I don't require it.
The flash also emits mnitor pre-flashes in certain modes, especially when used in conjuntion with other off-camera flash units, so as to get the exposures correct.
Possible simple answer : Nikon tends to use the AF assist lamp instead of the flash itself for red-eye reduction - so if your flash is set to red-eye reduction mode, the AF assist lamp will light up.
I don't use redeye reduction mode unless I have to - prefer to use flash off-camera, it works much better that way.