Yes, I have a similar issue, probably related:
I sync my DJS1000 up to my 2 CDJ3000s via PRO DJ Link via ethernet however, whenever I mix from one CDJ into the other the DJS1000 keeps assuming MASTER control.
Ideally when I mix one track into another on my CDJ3000s the MASTER should switch between the two CDJs only, with the DJS1000 only ever being in SYNC mode...
the problem is that when DJS1000 assumes 'MASTER' the CDJs lose the function where the active CDJ displays the other tracks waveform above
Surely there is a setting to ensure the DJS is only ever 'SLAVE' to the CDJs 'MASTER'?