Unfortunately that isn't always the case of getting perfect digital copies. Not much we can do except roll with it. Part of it was my fault because I had the tool and while I knew it could stretch the map to make grid lines fit better, I had always assumed in the past that the grids had to be square for the tool to work. I have fixed plenty of maps where the grids were square, just not uniformly created throughout. I never knew before the other day that I could take a map where the grids were 50 px wide and 56 px in height and the tool would stretch the entire map to make them all square. Pretty slick. I guess I just wish I had known this sooner - I would have fixed that map long ago.
Oh well ... I know now :)