I just wanted to share a tip that will help you get the best results from Mate References - I recently saw a case from a customer who was complaining of erratic behaviour with multiple mate references on a part. The mate references used each used a single, short axis as a common reference, and then other faces at various points along a shaft as the second reference in each case.
Since 2011, in order to improve accurate mate reference snapping behaviour, SW will consider the centroid of all of the selections as the 'centre of attraction' for that mate reference. So if you select geometry that is far apart from each other, the centroid will be at a distance from any of the geometry, and the mate reference will prefer to snap when you get near that point, rather than individual selections. By selecting geometry that's close to each other for a single mate reference, you will get the best behaviour.
In the customer's example, I edited all of the mate references, and replaced the axis with a cylindrical face that was adjacent to the other face in each case, and snapping behaviour was accurate and predictable.
I hope you find this helpful.