I get mail from two servers into my Thunderbird, one uses POP3 listen port 110, and the other POP3 listen port 995

Port 110 is used for normal POP3 mail and port 995 is used for POP3 mail servers that require an SSL connection. POPFile can handle both types of connection.

The POPFile wiki has a page that explains how to configure Thunderbird to make it use POPFile to classify your POP3 mail: Mozilla / Netscape / Thunderbird Configuration

To make POPFile classify your incoming POP3 mail some small changes have to be made to the account settings in Thunderbird.

It is easier to start with the account that uses port 110 as fewer changes need to be made.

I'll use 'pop.example.com' as the POP3 mail server name and 'myusername' as the User Name for the mail account.

(1) POP3 mail using port 110

(1a) Thunderbird settings for POP3 Account using port 110 without POPFile

Server Name          : pop.example.com     Port: 110
User Name            : myusername
Connection Security  : None
Authentication method: "Password, transmitted insecurely" or perhaps simply blank

(1b) Thunderbird settings for POP3 Account using port 110 with POPFile classifying POP3 mail

Server Name          : 127.0.0.1           Port: 110
User Name            : pop.example.com:myusername
Connection Security  : None
Authentication method: "Password, transmitted insecurely" or perhaps simply blank

Note: Only the "Server Name" and "User Name" settings get changed in Thunderbird for this account

(2) POP3 mail using port 995

The account that uses port 995 probably uses SSL which means more than just the 'Server Name' and 'User Name' settings in Thunderbird must be changed to let POPFile classify incoming POP3 mail for this account.

(2a) Thunderbird settings for POP3 Account using port 995 and SSL without POPFile

Server Name          : pop.example.com     Port: 995
User Name            : myusername
Connection Security  : SSL/TLS
Authentication method: Encrypted password

(2b) Thunderbird settings for POP3 Account using port 995 and SSL with POPFile classifying POP3 mail

Server Name          : 127.0.0.1           Port: 110
User Name            : pop.example.com:myusername:ssl
Connection Security  : None
Authentication method: Password, transmitted insecurely

Note: The "Server Name", "Port", "User Name", "Connection Security" and "Authentication method" settings in Thunderbird all need to be changed for this account

Adding ':ssl' at the end of the 'User Name' in Thunderbird tells POPFile to (1) use SSL and (2) connect to port 995 on the mail server. Nothing else in POPFile's configuration settings needs to be changed when using SSL for a POP3 mail server.

If you are not sure how to make these changes, ask for more help before making any changes to Thunderbird.