How do I get the message window to automatically clear after speaking in Communicator 5?

There's not a global setting for this but you can do it on the page itself.

1. Open the page that has the message window you want to auto clear after speaking.
2. Press and hold for 5 seconds or right click to bring up the Quick Menu.
3. Select Edit Page Set.
4. Select the message window.
5. Select the first icon under Special in the left toolbar.  It's called Smart Button Type and Actions.
6. Select Add.
7. Select the Message Window tab.
8. Select Clear.
9. Select Add.  Clear should now show up as the second option under Say Message.
10. Select Save.
11. Save your changes and go back to Run Mode.