Did you turned off the quantitize?
R1 - 1.08 - HotCue SYNC problem.
Steps to reproduce.
Find the right beat
save the A HOT-CUE by pressing A button.
Play your song and press the A button (in beat)
you will see first beat is skipped 80% of times.
We had similar problem when CUEying before - now for HOT CUES.
When you press A,B,C quite often the first beat is MISSED.
I have tried to reset the HOT-CUE, few times, manually, using little beat-grid, WITH or WITHOUT SYNC, WITH or WITHOUT MASTER , with or without second deck playing .
It was embarrassing yesterday - believe me. My R1 unit = is just expensive MP3/CD player!