I recently attempted bouncing tracks with AudioSnap applied and ran into the same problems:

- Horribly mis-timed audio when bounced to track (but the original file with AudioSnap engaged is fine)
- Glitches, pops, etc. when bounced to track (when the original does not exhibit these noises)
- Waveform disappearing and wont display even after deleting the Picture Cache or Recomputing Picture
     (will display only after I disable AudioSnap)

Also, I would like to add the following:
- Phasey sound of bounced track
- Average Tempo calculated shows 1264496104 (In Sonar X1).  WTF?
- Filter Resolution pull-down only allows "All" (In Sonar X1)

I performed a null-test, and confirmed that (obviously) the bounced audio is NOT the same as the original track with AudioSnap engaged.  I tried several variations of bouncing audio with the different render options, and all of them sounded equally horrific.

I work with Pro Tools as well, and must say that Elastic Audio works perfectly when rendered.  Elastic Audio and adding transient/warp markers is more time consuming than how AudioSnap implements transient markers, but it does work...

I'm running X1c  and I have also experienced some issues with Audio Snap Transients vanishing as I scroll along, or even the image of wave on the track vanishing while remaining audible. I was terribly mortified and confused when I began to see my work crumbling. I contacted support and it went so far as the CSR asking me to send him my full project so they could all have a look at what was happening, this after sending them a video detailing my experience. I was told that the above mentioned behaviour has not been observed before and I was not pleased to hear that........

I have noticed what seems to be causing this. I've noticed the "Average Tempo" dropdown list in the Audio Snap control window, the value has a tendancy to change on you. Thus, eliminating/creating transients and screwing with the wave view (odd).  In my mind I don't see why the value would change if the track was recorded in the project at the tempo you're using. As you all read this, is there any advice on how to fix this, how to stop the Average Tempo value from changing? Resetting the Average Tempo value makes everything reappear as expected and you can begin working normally from there.

My solution to all of this goes like this; 

I only experienced the above issues after saving and re-opening the projects. So now, before I close the program after working on Audio Snapping, I "back-up" my work by performing a "Bounce to Tracks" for all parts that I've worked on. This method takes a little more time before shutting down but it gives you peace of mind that your work is done and preserved, and it also writes the new wave with perfect stretching, no oddities in the audio as compared to listening back to the original Audio Snapped track.  

I'm off to go work some more on my current projects. Hope I've helped someone out here who's jaw has just dropped for the first time with this issue. :)