Well, I don't really know what happened.
It's not related it seems actually.
Indeed, when forcing the remove of jack, amnesia worked again. But it broke my system because libjack is required by many packages.
So I had to install it again so the game was again non functional.
However, I uninstalled - reinstalled version 1.0 and I don't know why, Amnesia offered me to restore default settings --> it made it work, even after updating to 1.0.1.
Well... Dunno. Maybe it was trying to use portaudio which itself tried to use jack ? Now it used Pulseaudio.
Really, I don't know. There was definitely something wrong, which made Amnesia segfault when the jack server was not started...
Works again