I'm on a Macbook Air with OSX 10.8.4. I've tried release 648, 649, and 725 of OpenNX to connect to Ubuntu 13.04. Each didn't work out of the box and even with the above trick of editing my profile's cfg, my keyboard mapping still isn't right. (The sshlog shows '--keyboard="empty/empty"')
Once connected, in all of these cases, the 'd' key minimizes all open windows, the up arrow key maximizes the current window, and the down key restores it to its original size. My point is that with all of the above attempts changing something on the Mac OpenNX client, I'm starting to think the problem is something Canonical has done with Ubuntu 13.04 and/or FreeNX. That latter doesn't look like its been updated since I had to install it from the 12.xx ppa.
As a further datapoint, even X2Go connections exhibit the exact same behavior when using the Gnome desktop. In the X2Go case, the client dialog shows using a pc105/us keyboard.
I hope this gives others something to go on. I couldn't add this as a comment so had to do it as an answer, sorry.