johntheripper-1.7.2-r1 has various problems with its configuration, even after reemerging it. (The residual /etc/john and $HOME/.john directories were removed manually after the package was unmerged to ensure a clean build.) After cracking the first password, john fails with the following error: fopen: /etc/john/password.lst: No such file or directory Touching this file allows john to continue, but not for long: fopen: /etc/john/all.chr: No such file or directory password.lst and all.chr are actually stored in /usr/share/john. The 1.7.2-r1 ebuild includes: -DJOHN_SYSTEMWIDE_HOME=\\\"\\\\\\\"/etc/john\\\\\\\"\\\"\" which explains why it is not looking in the default location /usr/share/john. If this is intentional, password.lst, all.chr etc. need to be moved to /etc/john.
Thanks! Sorry about this... This package had gone a major cleanup.