The top menu bar in macOS is supposed to show the currently focused application, and its associated menu entries. This works fine for ThinLinc's login window, but fails to work properly once connected. macOS keeps showing the previously focused application, so it doesn't seem to properly notice the switch to our window. It probably has something to do with the magic we do to run multiple processes as the same application.
This can be seen in attachment 1021 [details] from bug 7832.