@Mick > How do you have the audio connected from the DJM-900NXS2 to the DJS-1000? Do you have the DJM SEND outputs connected to the INPUT on the DJS?
And then how do you have the return connected? Is the OUTPUT from the DJS connected to one of the channels as a line input, or do you have it connected to the RETURN?
If you're using the S/R loop, you'll need to select the sampling source from the FX channel selector, then engage the S/R ON/OFF button.
If you're using an AUX loop, the same applies as above, but you'll also need to set one of the DJM channel inputs to AUX RETURN to have the audio come back into the mixer.