In order for annotation to work on Keynote, Keynote needs to allow Splashtop Whiteboard to draw on top of it. You need to enable this feature in keynote, "Allow Exposé, Dashboard and others to use screen"
Note: This requires Splashtop Whiteboard 126.96.36.199 or higher and also Mac Streamer 188.8.131.52 or higher.
1) Open Keynote Preferences
2) Select the Slideshow tab and check the checkbox labeled "Allow Exposé, Dashboard and others to use screen"
3) Congratulations, your Keynote is set up to work with Splashtop Whiteboard!