ISSUE
When you import a video into Adobe Media Encoder CS4, add cue points, and then export the video using any of the F4V profiles, the cue points are missing. Exporting the same video to FLV works as expected.
REASON
Cue points are a feature of the FLV video container format. FLV is a proprietary format developed specifically to complement Adobe Flash.
The F4V format is based on the format specified by ISO/IEC 14496-12: ISO base media file format which is not specific to Flash and does not have native support for the cue points that the FLV format uses.
Read more about these formats at the FLV/F4V Technology Center (http://www.adobe.com/devnet/flv/).
SOLUTION
Do one of the following solutions:
If you need to use the cue points generated by Adobe Media Encoder, encode your video in FLV format.
Add the cue points to the host SWF either using ActionScript 3 or, if you’re using a FLVPlayback Component, add the cue Points in the Parameters tab of the Component Inspector. For more information, see the section “Use cue points” in the Using ActionScript 3.0 Components > Using the FLVPlayback Component chapter of the online help.
Source: http://www.adobe.com/go/kb405265
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