Waypoints garbled in Mission Planner when reading from the ground with a mission onscreen

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What steps will reproduce the problem?
1. Load a small 3-5 waypoint mission in mission planner and write WP to 
aircraft.
2. Click Read WP
3. The waypoints read back will not include one or more of what was loaded and 
sometimes have incorrect altitudes.
4. If I manually clear the mission in MP and then read WP the correct mission 
is loaded back from the aircraft indicating it was actual sent and stored 
correctly - the problem seems to be in the readback to MP.

What version of the product are you using? On what operating system?
MP 1.3.0 on Windows 7
APM Plane 3.0.1 on Pixhawk with 3dr Radios
(Tried re-flashing to Copter V3.1.3 and saw same behavior)

Please provide any additional information below.

Original issue reported on code.google.com by dellarb@gmail.com on 23 Apr 2014 at 10:25