Due to permission issue with /var/run/snort folder (where /var/run is symlink on /run, and /run is mount point for tmpfs partition), pid file can't be created. Log message: ... Set gid to 996 Set uid to 107 Checking PID path... WARNING: /var/run/snort is invalid, trying /var/run... Previous Error, errno=13, (Permission denied) WARNING: _PATH_VARRUN is invalid, trying /var/log/ ... WARNING: /var/log/ is invalid, logging Snort PID path to log directory (/var/log/snort/). Writing PID "52289" to file "/var/log/snort///snort_eth0.pid" ... In ebuild we have (src_install function): fowners -R snort:snort \ /var/log/snort \ /var/run/snort \ /etc/snort But, since /var/run could be symlink on /run (by default, tmpfs partition), permission for /var/run/snort can't be stored during system halt/reboot. So, /etc/init.d/snort script create /var/run/snort folder with root:root owner and 775 mod all the time, and snort user can't creat pid file in that folder. The posible solution is correct /var/run/snort folder creation part in /etc/init.d/snort script: replace "checkpath -d /var/run/snort" line on "checkpath -d -o snort:snort /var/run/snort" fix the issue. Reproducible: Always