Embed interactive SWF in PDF - losing interactivity

I have a simple swf file that has multiple squares that change color when clicked. I need to embed it into a PDF so when viewed, you can still click the squares to change the colors. However, when I embed it, the squares no longer change colors when clicked. The PDF is built in Indesign CS6 and I have tried embedding the SWF file both in Acrobat Pro and in Indesign, both with no luck.
The SWF file actually ahs multiple instances of the same swf file loaded into it and it works fine when tested in a browser and in Flash and also when I open it from Windows Explorer.

Have you attached those child SWFs to the resources collection for the Rich Media Annotation so the parent SWF can load them?
kelsey.peterson wrote:
The SWF file actually ahs multiple instances of the same swf file loaded into it .

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