I figured out what was the problem. For some reason, after you upgrade to a newer version of ispconfig, the apache vhost file for domains will not be upgraded based on new apache vhost template files that ship with new ispconfig version. To get the apache vhost config files updated I had to disable PHP for each domain, run /usr/local/ispconfig/server/server.sh manually then enable php in ispconfig for each domain and run /usr/local/ispconfig/server/server.sh again. This worked for most of the domains, not for all.
Is there a better way to force ispconfig to regenerate apache vhosts for all domains?