Squid also allows you to permit and reject ports: see /etc/squid/squid.conf
Sample:
Code:
acl Safe_ports port 80 8080 # http
acl Safe_ports port 21 # ftp
acl Safe_ports port 443 563 # https, snews
acl Safe_ports port 1025-65535 # unregistered ports
Is your config permitting POP and SMTP?