Sonar X3... I went through a whole bongo track and aligned up the beats/transients. when I went back to the beginning of the song, most of the transients are not visible. as I drag my mouse over the visible transient, they disappear, yet some stay. and some are adjustable while others disappear while I swipe my mouse horizontal across the track. adjusting the intensity does not fix the problem. Has anyone seen this type of flakiness? Is audio track a flaky tool that can ruin a track?

I thought most of the graphical glitches with AS transient markers had been fixed by X3e. When it does happen, changing zoom level will usually make them visible. I've never seen Audiosnap move a transient without being commanded to in some wa, so on that basis I would say, no, it won't ruin a track by itself.
 
If graphical issues cause you to mistake which transient goes with which beat or if the changes you make are too radical or based on misplaced markers, the results can be bad. But so long as you don't render any changes permanent, you can always reset markers or disable Audiosnap altogether and try something else. That said, it's always a good idea to start with a copy of the project (or of an individual track that you want to snap) so that you can easily fall back to the un-snapped version if you don't like where it's going.
 

And/or you could play it again, but this time do it on time.  I believe the truth is that Audiosnap can SOMETIMES fix some sloppy playing, and sometimes you just have to do it over, and over, and over, and over, and comp it altogether if that's what it comes down to. 
 
You can glue a broken cup back together, but it always looks nicer if its never been dropped.