Which sets of points, the blue dots or the purple hexagons, did you create using 10 SP4? And the other set of points were produced by 9.3.1?
As the image shows what's expected, the Inside points are not necessarily at centers. May I ask what made you to choose the Inside option instead of the centroid option (uncheck Inside)? For comparing shape changes, if the parcels have unique IDs or attributes and the changed parcels carry the same original IDs, then centroid points would be more reliable, even if they fall outside of polygons; you just need to make sure you compare the centroids with the matching attributes. Could that work?