I think in configuration tab, and units are cm, so 10000 is 100m.
Cm makes sense, but I couldn't find it in the config section, so assume it must be the default altitude used in the flight planner section.
The thing that was confusing is we had set the APM planner to feet, but obviously the apm only uses metric. It caused some unexpected altitude changes when using auto until we worked it out!
Thanks for your help :)