Finally got around to getting back on the CNC, took a break to work on the race car we broke a crank on. Anyways, I could go back and write down the numbers measuring both sides of the 1-2-3 block in both X and Y but its not too relevant the exact numbers. It certainly was as people said here effected by min travel before activation.
So thinking about my machines backlash (0.0015-0.002") I reduced the 99 offset diameter from 0.125 down to 0.114. Its pretty interesting and Id like to think this is a good way to compensate, will evaluate after a few more parts. But it certainly goes to show we should really thinking about tool paths and have important dimensions cut from one side/setup.