Truecrypt installs and runs but is unable to use the Unity system tray for the program running in the background. If one exits the main program can not be restarted to unmount the encrypted volume(s). I have tried white-listing 'truecrypt' but it still does not allow the background program to appear in the system tray.
I had a query on this issue also. This is what solved the issue for me using 11.04.
Open terminal and paste in the following:
Then log out and back in to Ubuntu, you should see a small Truecrypt icon up by the connection/time/audio icons are in the top right corner. Use this icon to open/close the application as per normal, not the Unity interface
open your terminal, then run:
after add 'truecrypt' word (it is case-sensitive!) this list and set it.
['JavaEmbeddedFrame', 'Wine', 'scp-dbus-service', 'Update-notifier']