NAIPS returns a "missing waypoints error" but nothing obvious is missing.

This will occur if on an IFR plan you depart or arrive at an airport via a designated route and you do not enter the arrival/departure via the associated naviagtion aid. For example:

YMMB W661 ML H129 DOSEL W569 SBG W569 YMAY


Airports (YMMB and YMAY in the above example) are not on the designated routes (W661 and W569), their associated navigation aids are. When submitted flight plans went via briefing officers (by phone/fax or via NAIPS), they knew what you meant and inserted these waypoints for you. Now NAIPS plan submissions go direct into TAAATS the onus is on the pilot to get it completely and technically right. The correct route for the above example is:

YMMB DCT MB W661 ML H129 DOSEL W569 SBG W569 AY DCT YMAY


Command Flight Planner tries to identify and insert the arrival/departure via navigation aid waypoints automatically.   However, under some circumstances the program cannot do this.  You can force Command Flight Planner to rethink the route: after you finish entering your waypoints click on the "Revalidate & Identify all IFR Routes" button immediately above the flight plan entry grid.  This action will insert missing navigation aids.