I upgraded to X1 Producer over the weekend (without a hitch!) but I had this problem in X1 Studio as well.
Using AudioSnap, I copied a mic-recorded kick drum track to a synth track with SD3. All the MIDI notes and associated velocities are there, but when I solo-play it back, it skips over some of the notes as if they're not there. When I sample those specific notes in the Piano Roll view, they work ok, but a full playback seems to cut notes. Anyone seen or had this issue?