@Nik > Few questions, what version of Traktor are you using?
Have you updated the firmware on the players? Firmware available here: http://pioneerdj.com/support/product.php?lang=en&p=CDJ-350&t=96
What computer are you using (specs / OS) etc?
You might have to try adjusting the latency settings, its not necessarily a case of having it at the highest possible setting.