I think it may have to do with the rotation of the bit as it grabs the material will torque the machine ever so slightly. At least that's been my experience. Or else the pieces aren't the same thickness, or there's a slight deformation in the table or material.
When I built my cabinets I used dados on the gables, with the dado depth the same as the material. The boxes squared up much more easily. I then glued and screwed from the tops/bottoms and sides where necessary. There are videos on YouTube from a guy named Woodman. It's a 64(?) part series. Long, but I learned a lot.
Before I got the domino, I would use dados or rabbets and screws to build cabinet boxes. After the domino, I built them using butt joints with dominos for alignment and extra glue surface. When using prefinished maple ply, I use the Titebond melamine glue instead of the regular wood glue which isn't suitable for a non-porous surface. http://www.titebond.com/product/glues/c9121dfd-2a9d-46d0-bd6d-c183e64bd0cd
When I was looking into it, another thing that came up in searches was Roo glue.
Dowels, biscuits and/or screws work too. I prefer to avoid the arithmetic involved with dados, personally. Commercial shops are using a tossup of dowels (w/case clamp), CNC dados, and Confirmat screws for a lot of frameless cabinets these days.
In Europe it tends to be dowels, Dominos or screws (NO pocket holes, though) for pre-builts. A few smaller shops use biscuits, but not many. Nobody here ever uses rebates ("dados") or pocket holes - far too time consuming and confer no advantages - but then we tend to use MFC for carcasses and that doesn't work well with either of those techniques
