My guess, and this is only a guess, is that the GPS in the airplane doesn't have the procedure programmed in like it is on the chart, but rather has the precise location of the waypoints programmed in. Then the unit (or the computer that programs the unit) has the waypoints connected together in the correct order and calculates its own heading information. The difference is either a rounding error in the computer or an error with the paper chart.
But that could be completely wrong.