This is audio or MIDI?  I have never had this behavior with MIDI and would be at a loss to explain how it would even happen.  Assuming you must mean audio.

I think he said MIDI. Which is strange because quantizing it should surely move the notes to the proper beat markers. 
 
I wonder if notes other than the first note in a clip are also off-time by a slight amount?
 

I've had this happen on midi too. It's easy to see how it could at the end of the clip. I'm not entirely positive how it happens at the start of one. Does quantize actually change clip length?

yea it's all MIDI. very strange indeed guys. i just had it happen this morning. recorded. quantized to 1/8th notes. found the bars that i wanted. with snapping on i selected the beginning of the first bar of the loop, split. selected the beginning of what would be the next bar after the loop. split. deleted everything before and after. drag a copy to the next bar. play back. it's clearly off. i go look, and it's like 04:01:078 or some random little tiny number like that (i don't remember what the exact number it was). so i delete the copy i made. right click the original quantized and chopped out clip, hit apply trimming. drag it so it's basically right on top of itself but its actually bringing it back that tiny little fraction of a beat back to the 04:01:000. then from then on i can drag copy copies of the loop with no problem. but its like either the quantizing or the snapping just isn't working right. and my workflow hasn't changed at all since sonar 8.5 (and before that) and i never had this problem in pre-X versions of Sonar...

Yep . . . I get this too. Was working yesterday with midi clips arranging a song, and snap settings (with regard to cutting and pasting) do not always work like expected. As stated, if you use "apply trimming", then you are usually snapped to the first note of the clip, but it's an extra step that I don't need.
 
So . . . I look at the snap, magnetic strength, snap to landmarks events, copy and paste special settings, snap to, snap by,  . . . Ya I like options, but maybe there's too many settings to make something simple more complex.
I try not to tinker too much with default settings, and when I do, I always try to put things back where they were.
 
To be specific, the midi clips I'm manipulating are tracks with Soft Synth VSTi's inserted as simple instrument tracks.
(If that makes any difference)
 
My workflow for working with these clips: SELECT CLIP - SHIFT-G (snaps to beginning of the clip) - Ctrl-C -
Key Command "G" (go to - specify bar + time location) - Ctrl-V
 
 . . . however, SHIFT-G snapping to the beginning of the clip is not always snapped to the first note of that clip, so "apply trimming" must be used. Just wish I could pinpoint why this method works on some clips, but not others.