Official comment
So I have a bit more insight into this issue for everyone...
If you play the same track on 2 x XDJ-1000, the 2 tracks may not be in sync. This is caused by variances of the system locked oscillator used in each XDJ-1000. This is the current status of how XDJ-1000 works.
If you play the same BPM tracks on 2 x XDJ-1000, the 2 tracks may not be in sync. This is caused by the BPM analysis accuracy and is currently under investigation for improvement.
The LOOP and the played track may not be in sync. This is caused by the accuracy of BPM and LOOP. This is the current status of how XDJ-1000 works .
As BEATGRID is managed by ms, mixing a LOOP with Master Tempo on will be drifted when SYNC is not used.
If 0.3msec gap, which is rounded, exists, one loop will generate 0.3msec every time a one-beat loop is played and this gap will be accumulated. For example, 4.8msec of gap will be generated by mixing for 4 bars (16 beats). This is corrected when using the SYNC function.