There were two servers that didn't have Tor running, which obviously is needed for the transparent .onion thing to work. I started Tor on both of them and checked .onion resolution, it should be good now.
Also checked all the other DNS servers using the Perl script @ https://cryptostorm.is/checkdeepdns.txt
and it reports that everything is now working correctly.
If you still can't access .onion sites without Tor Browser, then check your DNS settings to make sure your system is using the DNS IP that's pushed by our OpenVPN server. In the widget's black output window, there will be a line that looks like:
Wed Aug 01 14:26:55 2018 us=112601 PUSH: Received control message: 'PUSH_REPLY,register-dns,persist-key,persist-tun,redirect-gateway def1,redirect-gateway bypass-dhcp,dhcp-option DNS 188.8.131.52,block-outside-dns,route-gateway 10.54.0.1,topology subnet,ping 20,ping-restart 60,ifconfig 10.54.246.226 255.255.0.0,peer-id 0'
The IP after "dhcp-option DNS", 184.108.40.206, would be the DNS that my system is using. It's different for every node, but whatever IP is in that line should be what your system should be using for DNS. Check with https://dnsleaktest.com/
to make sure that it matches.