I have found that following these instructions
https://doc.pfsense.org/index.php/Why_can't_I_query_SNMP,_use_syslog,_NTP,_or_other_services_initiated_by_the_firewall_itself_over_IPsec_VPN%3F
click System > Routing. On the Gateways, tab, click + and add a gateway using your LAN IP address (check the box to disable monitoring). Save/Apply,
then go to the Static Routes tab, click +, enter the remote VPN network in the "Destination Network" box, select the LAN IP gateway that was created before, and add a description
if you want, then Save/Apply.
Once i removed the manual route, rebooted pfSense. My ubuntu machine was able to communicate thru the tunnel.
Why this stopped working all of a sudden is a mystery.
Also, I am directing the pfSense Syslogs thru the tunnel to a remote syslog server and since removing the manual route, it is not working.
Any suggestions would be appreciated.