Hi Fwarton,
This may be difficult to guess from our end,
particularly since you built your own version.
So you are currently running either NeuroDebian
AFNI or your own build? Consider trying one of
our builds, such as:
http://afni.nimh.nih.gov/pub/dist/tgz/linux_openmp_64.tgz
At least you can easily see how that goes.
- rick