The problem is quite the opposite. Any new server that I deploy automatically has the DSM plugin enabled despite the fact that my deployment profile has the "use DSM plugin" box unchecked. It is also ignoring the checkbox that hides the VNC icon in the system tray.
I tried re-creating the deployment profile, removing, and re-pushing the server to several clients, and the settings just don't seem to work properly. I've since downgraded to version 2008.4.4.213 and the problem has gone away. I can push new servers without DSM, and the tray icons are once again hidden.
Just so you know, I installed a new copy of VENM for another admin who is starting to use the tool aswell, he has also has the exact same problem.