I'm not running any of the containers on the system, so it doesn't look like a permission issue.
I looked at the
libx2go-server-db-sqlite3-wrapper.pl and /usr/share/perl5/X2Go/Server/DB.pm and just ran perl commands to add a new port to used_ports table. It worked (as root) and I can see the new entries in x2go_sessions. However, nothing is added when I connect from remote server using x2go.
Since nobody else seems to have this problem, it's probably something related to my system, although I checked all the libraries and file permissions. I finally gave up an switched to postgresql backend. It was a pain to configure, but it works and I can suspend and restore connections now.
Thank you.