SWF movies that are in PDF files which were exported from InDesign CS3 or CS4 will not play in Acrobat or Adobe Reader version 8.x or 9.x.
Acrobat or Adobe Reader 9 display "Buffering..." in a dialog box, but the movie will not play.
Acrobat Reader 8.x fails to play the movie with no other feedback.
You updated your version of QuickTime and/or Safari.
Your current Mac OS X system doesn't have QuickTime components needed to play SWF files within Acrobat/Reader in a Screen annotation type layer.
In PDFs produced by InDesign the SWF file is contained within a "Screen" annotation type. For this annotation Acrobat 8/9 uses QuickTime to play SWF files. Acrobat 9 introduced a new annotation type, "Rich Media", which can utilize Acrobat's built-in Flash Player to play SWF content, and thus avoids the QuickTime player incompatibility.
However InDesign CS4 only exports to "Acrobat 8 Compatibility" with the "Screen" annotation. Because the "Rich Media" annotation is new to Acrobat 9.x, it will not be understood by PDF viewers that can only read up to Acrobat 8 Compatibility. Thus, if you place the SWF file with Acrobat 9 into the PDF files, it will not be readable by Acrobat or Adobe Reader 8 and older versions. With the version 4.0 release of Safari appears to include QuickTime updates which re-enable SWF playback.