I have had this same problem when doing KJFK-KSFO in the MD-82.
Have you saved the flight to continue later and reload it? This is what happened to me.
MAKE SURE: All you waypoints are correct/Valid. Check for Any Discontinuaties or Vectors.
If it does not work, Check your waypoints again Using the "Plan" Screen.
If all your Waypoints are correct you can either:
Cancel the IFR Plan with the ATC and continue
Go direct to the Next waypoint you have. *MOST RECOMMENDED* Please use this one, it worked for me.
Also check if you are using the right FLP. When I had this problem, I was using the wrong flight plan (God knows how) so it took me straight to start THAT route. I ended up Diverting to KSEA and went on the ATC Route somehow...