I think quantize in rekordbox is a lit bit tricky too.
I was with the same problem, when i was playing with dvs two tracks (1st already playing) and using a hot cue to jump to the start of the 2nd track, this track looks like has your own clock. So, if the quantize step/snap was 1 beat and for some reason i've pressed a hot cue on the 2nd of beat from the 1st, the quantize consider only the 2nd track, every hot cue press will follow of beat.
I've deactivated quantize for hotcues. =/