Ok, so, I figured it out after an afternoon of frustration. The fact is, Sonar lets you zoom in so far that you will see the smallest ticks off and that is what I'm seeing. It's not really off enough to matter, the sync issues I could hear were actually found in a kick drum track that was off because the grove sync is not reliable.
I fixed the problem by taking a single one-shot kick sample, pasted it 3 times so it was a measure with 4/4 on the floor and then bounced to new clip. Then pasted that multiple times. Reproduced the original visual issue of the screenshot, but still had perfect sync. So Done, issue closed. Here is the feature request for cakewalk: either limit the amount you can zoom in or make the clips align directly to the line.