Never mind, figured it out ... Sleep doesn't work in scripts and it was playing both sounds.

Solution:
null=[] spawn {playSound3D ["a3\sounds_f\weapons\Rockets\explosion_missile_05.wav", player]; hint "sound played..."; sleep 10;hint "sleep finished..."; playSound3D ["a3\sounds_f\weapons\Rockets\explosion_missile_04.wav", player]; hint "second sound played...";};

Please close as not a bug... Or change to a bug Sleep doesn't work in activation script.