Just a guess here, but are you running Quantized tracks and have Quantize active on the decks? If so, then it could be just because the decks start playback based on the beatgrid rather than exactly when you press the Cue button. Not sure if the Cue buttons work that way with Quantize, but Hot Cue buttons do.
Try to turn of Quantize, there is a small button for that, and see if that makes a difference.