Get the Free version of UAV and download and examine every aspect of your flight logs.You may find unexpected problems.
I know I did. I tried to use Batch modify to set all my Waypoints ( in a complicated mission ) adapting the altitude to Ground level changes.
That was the start of my problems. It wasn't until I use the UAV data that I could see it really messed things up. I haven't figure yet how to undo it. but you can see virtually everything that is going on. It is an invaluable debug tool.