Non-Alignment of waypoints on Terminal Approach

I use FSX flight planner with updated Nav Data for Eaglesoft Citation X and have updated Mag Variation, but on final ILS approach the 2-4 waypoints before landing "don't align" like all the waypoints in the flight plan.Up to that point in the flight plan all waypoints are smoothly transistioned. The way points on the Primary Display (2.5M scale) show the path to be off-set slightly so the plane usually veers a bit to one side or another as it crosses the waypoint, picks up the path again, proceeds to the next waypoint, veers again etc. Does this 2-3 times until final approach point which always seems fine, and then onto landing. Everything works fine, do a nice ILS landing with GS etc. Is it the FSX planner? Seems the flight plan and the approach are working off different data sets.. Thx.