When recording a Mac Keynote presentation with animations, the animations don't show correctly when recorded with Camtasia. The build animations are not captured and are ignored. Is there some sort of option that needs to be turned on for this?
Others may have more detailed information, but the first thing I think about is your frame rate. I use Keynote all the time with Camtasia and don't encounter any problems at 15FPS. If yours is set for a lower number, that could be the cause.