CDJ 2000s & Traktor 2.0 issue

Hello. I have been using the 2000s with traktor for some time now and so far its good. I connect two cdj 2000s via agregate to a macbook pro. I do not use timecodes nor any audio interface. My concern is that when I transition from traktor to cd or flash drive so the nex dj can carry on, either traktor freezes or the sound stops altogether. The situation is even worse when trying to go from cds or flash drive to traktor which in this case as soon a deck in tracktor is assaigned, lets say the deck oposite to the one playing cd or drive, the sound stops and the player assigned do not start traktor. Would be great if those format transitions could be done without issues, the players flexibility will increase and users like me would be pleased. This conflict does not occurs when moving from cds to flash drives or vice versa within the same player. My point is not having to buy a native instruments interface when I could use the players as a stand alone multirole platform.

Thanks for your help.