Well either the Selective fwmark port 465 tagging never works?, or if it does indeed (though suddenly cease to) correctly force emails out via the WAN, then you should provide detailed diagnostics to fully substantiate what you mean by "seems to get lost"
The Solution seems to be some delays.
#!/bin/sh
sleep 2
ip rule del fwmark 0x7000/0x7000 2> /dev/null
ip rule add fwmark 0x7000/0x7000 table 254 prio 9990
ip route flush cache
sleep 2
# Route secure email port to WAN and not VPN.
iptables -t mangle -D PREROUTING -i br0 -p tcp -m multiport --dport 465 -j MARK --set-mark 0x7000/0x7000 2> /dev/null
iptables -t mangle -A PREROUTING -i br0 -p tcp -m multiport --dport 465 -j MARK --set-mark 0x7000/0x7000
# Route RDP port through VPN tunnel
iptables -t mangle -D PREROUTING -i br0 --src 192.168.1.16 -p udp -m multiport --sport 3389 -j MARK --set-mark 0x7000/0x7000 2> /dev/null
iptables -t mangle -D PREROUTING -i br0 --src 192.168.1.16 -p tcp -m multiport --sport 3389 -j MARK --set-mark 0x7000/0x7000 2> /dev/null
iptables -t mangle -A PREROUTING -i br0 --src 192.168.1.16 -p udp -m multiport --sport 3389 -j MARK --set-mark 0x7000/0x7000
iptables -t mangle -A PREROUTING -i br0 --src 192.168.1.16 -p tcp -m multiport --sport 3389 -j MARK --set-mark 0x7000/0x7000