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Hi Chris, this might not fix your issue but it will help you understand what's happening with your PDF.
When you embed an SWF into a PDF, it usues a native Flash player built into Acrobat/reader, regardless of whether the user has it installed on their system or not (good for all).
But what happens is the controls/interface for the flash object take over the input of your interactive PDF, what this means is that when an SWF object is active, it takes over any user inputs until the active element is deactivated. To simplify this, it's as if you've selected a text field and you're trying to type shortcuts on your keyboard, the text field assumes control of the input until you deactivate it.
Typically an embedded SWF requires a user to click it to activate but if you've selected 'play on page load' then you've circumvented this. However I'm guessing acrobat handles this request is simply by focusing the object for you to activate it (as if you've clicked it).
What's happening is the video/animation is ending but is still active and I'm tipping that presentation controllers use the same method of input as pressing the arrow keys on your keyboard to navigate the presentation which as I've explained won't work until the object is deactivated or a mouse click 'unfocuses' the object.
Try loading your presentation to the offending page, once the video/animation has finished, click with your mouse somewhere blank on the page. Then use your normal method of navigating the presentation (keyboard/controller). Does it resume?
Also try this; once the video has flninshed, right-click on the video object and click 'disable content'. You should notice that the controller/keyboard navigation now work.
It's a bit of a hack explanation but I hope it helps you realise the potential/pitfalls of interactive in PDFs.
My advice is 'keep it simple', its quite easy to see that we can make a PDFs like a fully animated flash document but that's not what its intended use is so problems arise.
One thing I can suggest if you must make this work is to re-program the PDF presentation controller. Instead of targeting whatever the keyboard command is, you can have it target the menu item that does the same thing.
View > Page Navigation > Next Page
By using the menu command it will circumvent the keyboard input method which is blocked by the SWF and enable you to continue on your way.
While you're at it, in Acrobat Pro, right-click the offending object with the object select tool and under the Launch Settings tab, change Disable When: to The page containing the content is not visible. This will help with any further issues when you're not actually viewing the page.