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?

No one?

Ross,
 There have been reports of notes being skipped (since 8.5) when the "midi prepare" buffer needs to be bigger. People have been recommending to set it as high as 500 ms. (I'm giving you 2nd hand info just so I can be "someone").
Bill B.

LOL, thanks Bill.  I'm guessing that's a preference setting, I'll poke around.

Was this ever resolved? I tried increasing the midi prepare buffers to 500 and then to 1000 and there are still midi notes being skipped.

This is nutsy. I am trying to draw in a kick drum line on the PRV and every few measures the playback is skipping like the first few notes of the measure. Whose bright idea was this new feature?

Bump, any thoughts at all on how to get around this issue?

I had a similar issue prior to X1d. It would skip notes on my sampled drum tracks just like you. I am 90% sure X1d fixed my issue.

That may be true but I have installed and am using X2. I did a recent install, so maybe there is a patch???

They have a quickfix patch for X2. I honestly can't comment because I ditched X2 and went back to X1. I didn't even have the time/patience to get to drum sampling.