I have been using Ubuntu 9.10 at work after switching from vista. After being (expectedly) disappointed with performance over VNC (via VPN) when logging in from home, I came across the NOMACHINE suite.
Last week, I upgraded from OS X 10.6.2 => 10.6.3 at home. After that, I also updated my NX Client at home to the latest version, as there were issues with recent changes in the OSX X11 setup that rendered the NX connection useless. At that point, everything worked fine.
Fast forward, I upgraded from 9.10 => 10.04 on my work machine the next day, and after coming home and trying to log-in remotely, I noticed that the "s" and "m" keys, when pressed locally, acted as if the meta key was being pressed on the remote machine. That is, the "s" key opens in the Ubuntu login menu (the power icon), and the "m" key opens the messaging menu.
I found some info on using xmodmap to remap keys, however, I can't even begin to fathom what keys I could remap to solve this issue.