Interesting you bring this up.
I found in Sonar 8 that at times Audiosnap would completely spazz out and transients would be placed completely wrong and I would have to do work-arounds because on the audio clips as they were, it would be unusable as you kinda describe. My work-around would be to bounce the clip down to the exact same thing (new clip, same audio... just to reset the transient detection on the new clip), and then I'd have to spend that 20 mins or so making sure all transients were properly placed/detected.
Lame. BUT in X1 I have not experienced this.
I always always always turn off transients on all tracks once I'm done and have pasted a track as midi events. I have to cause saving is then very slow. I rarely ever re-open the transient view after I'm done with this process though. My workflow is probably different than yours, so this is just what I've noticed.