I've been learning about Presenter today and when I publish the presentation, all my animations for created through PPT disappear when I pause the presentation and click on the slides instead... Is there a way to avoid this or a way to add the same animations through Presenter? It's only text boxes appearing at different times on the slide...
You need to have you animations cued On Click and then you can sync your animations with the audio using the Audio Sync tool or you can place the click markers in the correct location in the audio using the Audio Edit tool. Then when you publish the animations should play back correctly.
Some emphasis animations are not supported, so if you see strange behavior that is why.