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Hey Rich,
Did you possibly analyse a live drummer song in NORMAL analysis mode, or inversely, an electronic percussion song in DYNAMIC analysis mode? That can make the difference in having two songs stay in sync. Check that first and if you're still having problems, a video would help us better understand the exact nature of the problem.
Thanks!
This also happens to me often. I don't use sync and this happens completely at random, almost always when I'm practicing mashup routines with the same song for an extended period of time. Eventually one song will start to drift on its own regardless of the BPM, almost as if someone was constantly nudging the jogwheel. There's absolutely no way to fix it other than loading a new song then reloading the current one, or constantly rotating the jogwheel in the other direction to correct it. Sometime it even carries across songs and I end up having to restart rekordbox, but luckily that hasn't happened during a performance yet.
Note this isn't new to Rekordbox 6, I experienced this on 5 as well but it's never been fixed.