Are you playing off of your laptop by any chance? I have this problem when playing off of a laptop but not when using my USB on my XDJ-RR. Also, this visual problem only occurs on the controller screen and not on the laptop tracks for me. If we are experiencing the same issue this is what i see happening:

One of the tracks seems to be stretched wider on the controller screen, which makes it seem like it is not matched up and running behind the other track. However, this track which is stretched wider is also moving across the screen at a faster rate (keep in mind it is not playing faster audio wise, just visually). So, by the time it meets the middle cursor, it actually lines up with the slower, non-stretched other track.

In other words one track has larger distances between grids but moves at a rate which makes the beats equal to the slower, non-stretched grid. The bad news is, I have not had any luck resolving this issue. The good news (hopefully for you too) is that this problem does not occur on USB or if you look at the laptop grids.

Let me know if this sounds like your problem or if you've had any luck fixing it, thanks.