Change the gtk theme in the rootless session (floating window mode) in order to get the one you find the most comfortable. There are some utilities to do this on the command line, for example gtk-theme-switch . It is quite simple to use, e.g.

gtk-switch-theme2 /usr/share/themes/Glossy/

selects the Glossy theme. You can verify if it works by running that command in a terminal in an NX floating window mode session.

We suggest selecting a theme automatically by wrapping the command that starts your application in a shell script that runs the gtk-theme-switch2 command.

After doing "apt-get install gtk-theme-switch" you should be able to run the gtk-theme-switch2 command which generates an appropriate .gtkrc-2.0 file on the Ubuntu server.