I am using FM11 with Windows 7.
When I import a SWF in to Framemaker, it plays fine.
When I print to PDF, the SWF just appears as an image.
This is true if I Import By Reference or Copy Into Document. The Embeded Adobe Flash files in PDF preference is checked.
When you're printing to PDF, do you have the "Generate Acrobat Data" option enabled?
FWIW, you should be using the Save As PDF option with FM11. It works quite well nowadays. Just ensure that the AdobePDF printer instance is your default when working with FM. The SetPrint utility from Sundorne ( http://www.sundorne.com/FrameMaker/Freeware/setPrint.htm ) is quite handy for this.