Try re-orienting the origin in the CAM program so it's in the middle of the part, not at the corner. Then whatever edge you indicate off of, the zeros will be half the width (or length, or depth) of the block you're milling your part out of, assuming it's accurately centered in your program. The problem you're running into is that the right front corner you're using as a datum point becomes the left front corner in the flipped part, which isn't necessarily the same thing.