We are using alternate sshd configuration, i.e. not /etc/ssh/sshd_config on our thinlinc servers. This includes non standard ports and other security related configurations.
The "standard" sshd_config (port 22) is only used for management of the system.
A nice feature would be able to configure which sshd_config file to use for the @thinlinc-begin@ and @thinlinc-end@ configuration.
The workaround for us is of course to swap our files. /etc/ssh/sshd_config and /etc/ssh/sshd_config_thinlinc.