For the shaper to work properly, the infeed and outfeed fences must be
1. Square to the table
2. parallel and coplanar (in the same plane vertically AND horizontally
On the "gray" X31 models at least, there are set screws in the rear fence "bracket" which allow you to adjust the shaper fence orientation relative to the table top and to each other. Unfortunately, to get to them you must remove the extruded aluminum fence(s). Here's the set up on my '99 model X31.