Hi Andrew,
Sorry for the long delay.
I ran a test with X2Go Client 4.0.5.1, and the connection was successful. This is the output from the command-line ssh:
$ ssh 192.168.1.20 Test banner! Password: Last login: Sat Sep 17 09:43:55 2016 [mike@dropship ~]$
Note that the banner is configured with "Banner /etc/issue.net" in sshd_config.
Also note that there has been restructuring of our code, both before and after 4.0.5.1's release, to improve our handling of keyboard-interactive authentication. Specifically, commits 10405481 & c5ee1ba6 (2016-01-29, before 4.0.5.1) and 044f22fd (2016-06-19, after 4.0.5.1, part of bug #1027).
If you are still having trouble, please copy & paste the output from the command-line ssh. If you have Windows clients, use cygwin ssh. Also, please confirm that you are using "Banner /etc/issue.net" in order to display the banner.
-Mike