Hi Dan,
is it a response HTML or just normal HTML 5?
Could you tell me which version of Captivate do you have? Does the other party use same version of Captivate?
When you publish your course, does your buttons work fine, while viewing from the Computer?
Check the timeline, if those buttons are behind any other object that is blocking them. Also, check if there is any other interactive object on the slide like click box, or any other button, that has a pause enabled and pausing the slide.
For best practices while publishing for I-pads, please follow this article: http://helpx.adobe.com/captivate/using/publish-projects-html5-files.html
Thanks.