Like @woodsnipper said check your squares for squares. I was confused the other day when after I squared up my machine it seemed more out of square. Turns out the large framing square was noticeable out of square.
If you are using a framing square I would check out this video.
Also if your machine is just a little out of square and you are using the coupler nut method to protect your bearings, adding a washer (or two 
) can help bring it in. You can do less with a few layers of soda can. It is pain for me to unbolt everything because I essentially have to remove all the cable rails just to do a minor adjustment.
Lastly if you end up having trust issues with your square like I did. You can use this method to bring it into square. Note this only works with the coupler nuts at the rails.
- Get it as square as possible with the above methods.
- Set 0,0 to the center of your machine.
- Have your machine engrave a large rectangle with a V-bit about .30 mm deep.
- Mark the corners. (I found putting a push pin half way in at he back and sewing pin at the front helpful.
- Measure the distance between cross pins. The delta is approximately is how much one side needs to be shimmed out. I.e. if 3328 and 3330 mm. I would add two .
- Rehome y and set your zero to the precision offset
- shift your zero by 5 mm or so in the X or y.
- Repeat steps 3 thru 6 until you are happy with the result.
