Talking with the devs, it looks like the Protocol and App filtering on ClearOS 6.x is quite buggy and prone to crashing and is no longer supported. Their best advice is to remove as much filtering as possible to see if you can stabilise it then add the filters one at a time and stop adding them if one of them makes it crash.

Can you fix up your internal mailing first? It looks like system mails are going to the root user. Can you edit /etc/aliases and add or edit the line for "root:" so you should have a line like:

# Person who should get root's mail

root:		nick

If nick is one of your valid e-mail users. Then from the command line run the command "newaliases". Your user should then start to receive system e-mails.

Is this a 6.x system? It seems to be with ethX style interfaces.

Here's the LOG after i reinstall the protocol filter:

"May 15 07:05:01 yumexf1 servicewatch: sanity checking l7-filter ...
May 15 07:06:01 yumexf1 servicewatch: restarting l7-filter ...
May 15 07:06:01 yumexf1 mailfilter: starting up (sender=root@yumexf1.gw, recipients=root@yumexf1.gw, client_address=) ...
May 15 07:06:01 yumexf1 mailfilter: Failed to set recipient: 5.1.1 <root@yumexf1.gw>: Recipient address rejected: User u ...
May 15 07:06:01 yumexf1 mailfilter: starting up (sender=mailer-daemon, recipients=root@yumexf1.gw, client_address=) ...
May 15 07:06:01 yumexf1 mailfilter: Failed to set recipient: Mailbox unknown. Either there is no mailbox associated wit ...
May 15 07:10:01 yumexf1 servicewatch: sanity checking l7-filter ...
May 15 07:11:01 yumexf1 servicewatch: restarting l7-filter ...
May 15 07:11:01 yumexf1 mailfilter: starting up (sender=root@yumexf1.gw, recipients=root@yumexf1.gw, client_address=) ...
May 15 07:11:01 yumexf1 mailfilter: Failed to set recipient: 5.1.1 <root@yumexf1.gw>: Recipient address rejected: User u ...
May 15 07:11:01 yumexf1 mailfilter: starting up (sender=mailer-daemon, recipients=root@yumexf1.gw, client_address=) ...
May 15 07:11:01 yumexf1 mailfilter: Failed to set recipient: Mailbox unknown. Either there is no mailbox associated wit ...
May 15 07:11:13 yumexf1 installer: app-protocol-filter-core - installing ...
May 15 07:11:13 yumexf1 installer: app-protocol-filter-core - installing default configuration ...
May 15 07:11:13 yumexf1 installer: app-protocol-filter-core - enabling protocol filter ...
May 15 07:11:15 yumexf1 installer: app-protocol-filter - installing ...
May 15 07:15:01 yumexf1 servicewatch: sanity checking l7-filter ...
May 15 07:16:01 yumexf1 servicewatch: restarting l7-filter ...
May 15 07:16:01 yumexf1 mailfilter: starting up (sender=root@yumexf1.gw, recipients=root@yumexf1.gw, client_address=) ...
May 15 07:16:01 yumexf1 mailfilter: Failed to set recipient: 5.1.1 <root@yumexf1.gw>: Recipient address rejected: User u ...
May 15 07:16:01 yumexf1 mailfilter: starting up (sender=mailer-daemon, recipients=root@yumexf1.gw, client_address=) ...
May 15 07:16:01 yumexf1 mailfilter: Failed to set recipient: Mailbox unknown. Either there is no mailbox associated wit ...
May 15 07:20:01 yumexf1 servicewatch: sanity checking l7-filter ...
May 15 07:21:01 yumexf1 servicewatch: restarting l7-filter ...
May 15 07:21:01 yumexf1 mailfilter: starting up (sender=root@yumexf1.gw, recipients=root@yumexf1.gw, client_address=) ...
May 15 07:21:01 yumexf1 mailfilter: Failed to set recipient: 5.1.1 <root@yumexf1.gw>: Recipient address rejected: User u ...
May 15 07:21:02 yumexf1 mailfilter: starting up (sender=mailer-daemon, recipients=root@yumexf1.gw, client_address=) ...
May 15 07:21:02 yumexf1 mailfilter: Failed to set recipient: Mailbox unknown. Either there is no mailbox associated wit ...
May 15 07:25:01 yumexf1 servicewatch: sanity checking l7-filter ...
May 15 07:26:01 yumexf1 servicewatch: restarting l7-filter ...
May 15 07:26:02 yumexf1 mailfilter: starting up (sender=root@yumexf1.gw, recipients=root@yumexf1.gw, client_address=) ...
May 15 07:26:02 yumexf1 mailfilter: Failed to set recipient: 5.1.1 <root@yumexf1.gw>: Recipient address rejected: User u ...
May 15 07:26:02 yumexf1 mailfilter: starting up (sender=mailer-daemon, recipients=root@yumexf1.gw, client_address=) ...
May 15 07:26:02 yumexf1 mailfilter: Failed to set recipient: Mailbox unknown. Either there is no mailbox associated wit ...
May 15 07:30:01 yumexf1 servicewatch: sanity checking l7-filter ...
May 15 07:31:01 yumexf1 servicewatch: restarting l7-filter ...
May 15 07:31:01 yumexf1 mailfilter: starting up (sender=root@yumexf1.gw, recipients=root@yumexf1.gw, client_address=) ...
May 15 07:31:01 yumexf1 mailfilter: Failed to set recipient: 5.1.1 <root@yumexf1.gw>: Recipient address rejected: User u ...
May 15 07:31:01 yumexf1 mailfilter: starting up (sender=mailer-daemon, recipients=root@yumexf1.gw, client_address=) ...
May 15 07:31:01 yumexf1 mailfilter: Failed to set recipient: Mailbox unknown. Either there is no mailbox associated wit ...
May 15 07:31:57 yumexf1 firewall: Starting firewall... ...
May 15 07:31:57 yumexf1 firewall: Loading environment ...
May 15 07:31:57 yumexf1 firewall: WARNING: l7-filter is not running, disabling protocol filtering. ...
May 15 07:31:57 yumexf1 firewall: Detected WAN role for interface: eth0 ...
May 15 07:31:57 yumexf1 firewall: Detected LAN role for interface: eth1 ... "

Can you see anything in the messages and system logs when it stops or when you try to start it?

Currently the filter is waiting an update and is not brilliant at the moment anyway. I am hoping for an update over the summer.