To get help with it, you'll have to be more specific about the ways in which the PDF "goes haywire."
What viewing environment(s) are you using to evaluate the result?
How exactly does the result differ from your expectations and/or understanding of the features used?
By viewing environment, John means, what PDF reader are you using to view the results?
The PDF goes haywire in terms of the panels that appear (from using the show/hide function on a separate button) flash on and off, and sometimes the close function doesn't respond, sometimes other buttons randomly disappear.
I have tried locking the layers before exporting, reducing the res, it still goes crazy.
I am using both Acrobat Pro DC and Reader XI. Exporting the SWF and replacing into a PDF is not an option since the end users don't have flash player.
The end result I wanted was a smooth, app-like motion, where you click on a button, it shows a panel which has hyperlinks in it, and a close button. There are between 8-12 buttons on the page, when you click them they all show a different panel, with different hyperlinks in the text. All the hyperlinks are their own separate button by the way!
Did you consider to use Publish Online instead and allow the viewer to download a PDF on demand?