I think it somehow demarcates the areas where various frames overlaps.
I had it once a long time ago. When u flatten all the layers, those lines should not be visible.
If there wasn't sufficient overlap for PS photomerge to calculate and merge the common points,
the pano would not even be formed.
The "crack lines" are still there in CS4, but only when the multi layer image is viewed smaller than 100%. When viewed at full size, or flattened as giantcanopy mentioned, the lines are no longer visible.