Well, this is the result of Sonar retaining the original time stamp from the track out of which the clip was selected and copied. If you cut it instead of copying, no problem. Or if you export/import the audio, or bounce to clip, OK, no problem.
But spending a day figuring this out is a problem while people were waiting for me to clean up a bunch of scratch tracks to build their session off of. And it is a programming error, as a clip copied and pasted elsewhere is no longer in the same musical context and could never be assumed to have the same placement in time. Sonar is oddly the richest, most functional DAW out there while at the same time always seeming to be as buggy as a roach motel at every turn.
I suppose I have learned to think of it as heavily nuanced, as once I have figured out exactly how it does work, it usually does that very consistently and well. And as obtuse as it first appears, Audiosnap is pretty cool. C'est la vie...