I've always taken the preview with Captivate and Presenter with a grain of salt. They seem to be mostly accurate, but, since they are not the final output, they can have some inaccuracies. Captivate has seemed to face this more in the past (I can't speak too much to it now since I just don't that feature much), but publishing locally and viewing the content has always worked to give an honest idea of what is or is not working.
As to the hyperlinks, did they get a shadow or any other formatting done to them? That can cause them to no longer work when Presenter converts the presentation to Flash.