Group,
I was experiencing repeated crashes when simulating my local flight plan. I had SRTM data pulled for my region and found this to be the cause of the negative AGL figure.
The wiki makes mention of a -noground argument for the ocaml sim script here:
http://paparazzi.enac.fr/wiki/Maps#Getting_and_using_SRTM_Data
Unfortunately, the script is rejecting '-noground' and does not list it as an available commandline argument.
For the time being I have deleted the SRTM data files from the data folder and my flights now behave as expected.