How about providing the log so we can have a look at it?
There it goes! :)
The MixAlt in the GPS log looks wrong to me - its reporting -21474836.0000. So if you graph GPS_ALT, you'll see that it reports a steady decrease in height. Is your barometer ok? Try the altitude test from the test menu on the console, perhaps...
This is the altitude test...
Finally reached 1.80m (the copter is always on the table)
You should do the full reset procedure as documented in the link and try again. Don't fly with it in that state.
I don't see the post about Mission planner displays altitude of 21 million or NaN appearin.... the links is OK?
In short it's caused by a bug in an older version of the mission planner (so please update to at least 1.2.34) which exposed a bug in the arducopter calibration code. I'm afraid you will need to go into the cli and type "setup", "reset", "Y" and then re-do your configuration. Sorry for the troubles.