From the picture it looks like you have vertical racks with plenty of chip debris collecting on them. That could be one source of inaccuracy.

If the two tracks that your gantry run on are not parallel, then it could be squeezing or pulling the legs of your gantry apart. This could cause the gantry to flex more when at one side of the table, and a flex in your gantry would result in the travel of the tip of your end mill increasing or decreasing during Y travel. That could be an explanation to the differing Y measurements of your squares.