Hi Francois,
Ok, I will repeat it in my next trial and see how things work and report it back if there would be any different encounters. All I remember, there wasn't any process seems like going on at the Matlab command window, because I have seen the messages saying the segmentation has done, but I will check again.
Ok, this is how I was doing to stop the whole process and then copy the files and folders in tmp folder, I have reports from such an incident, so here you can download them if you would like and if that would help somehow but it doesn't elaborate so much info anyways.
As I mentioned the only harsh consequence of it, if you do not copy the produced files manually they are gone with the closure of the brainstorm, so even though the whole process runs without a problem, since the ending is not properly works, it makes you unconfident about the whole process hence there is a risk of losing the whole produced segmentation files. I hope I can repeat it again and get better screenshots since I didn't get it in my last run, I also started to think whether it is subject data related or not, so I will check it with the same and other participants again.
It is my pleasure, I would be happy if I can help a tiny bit 
Bests,
Isil