2 at once

I'm finding that very often when I interfere with the top two songs in the playlist by inserting / moving / deleting entries, the CDJ will get the currently playing entries confused, regularly skipping a track, and playing two at once. Even hitting stop on one of the players won't get the CDJ back in sync. It can still ending up playing 2 at once after the current track finishes. Basically it means I can't change the next cued track without a high risk of having the CDJ play 2 at once, and it won't always get back in sync just by stopping one of the players.
I have 3 CX-250 players running, if thats of consequence.