Hi. I’ve come to this forum with the same problem. I’ve been able to find a solution (which works for me) with the info in this thread. I like to share this with you beautiful people.
The origin of the problem is in the “Phasing” of the track, as mister Bill Stanley mentioned above. However, you can adjust the phase of the playing track on the fly.
For those who do not understand; Every four beats are counted by the app and displayed in the wave mode as lines. The first of the four beats is a yellow line. Sometimes the app gets the phase mixed up and thinks the second beat is the first one. This creates the problem with syncing the two tracks, making them off-beat.
Again, as stated by mister Bill Stanley above, you can use the pencil icon in wave mode to set the grid correctly. This can be done on both decks, whether it’s playing or not.
If you’re setting it on the non playing deck, just drag the wave to the right beat and press the pencil and SET.
If you’re setting the currently playing deck just press the pencil icon and wait for the first of the four beats and tap SET at the right time to change it.
Hope this helps!