(sorry this is late hope you see it)
If the two X sliders are not square to Y or the two Y sliders are not square to X statically/before the steppers are activated then they will never be square. It you force them into squareness manually or with some sort of a jig like http://www.thingiverse.com/thing:930286 then it will stay square as long as the steppers are activated.
Of course it is best to have the axes square beforehand so you don’t have to tweak them each time you start cutting. I just did some light sanding on the X and Y sliders to tweak them square and was careful when tightening the center assembly. Mine stays quite square without having to check it before each cut.