Video Freezes when overriding flv files on FMS server

I have an flash application that captures a web cam video stream and stores it on the FMS server.
I notice when I create a brand new video, and store it on my FMS server, it works fine.
When I make another video and my application overrides the file with the new video, this is where I get problems.
When I download the flv file from the FMS server, and I play it locally it plays fine, but the timeline is weird.
The web player freezes the video during that first 15 seconds.
A 30 second video, will have a time line of like 45 seconds, the local flv player is smart enough to skip over the paused part of the video.
You will see it skip over the timeline to the good video (from 0sec to 15 secs). The web player freezes the video during that first 15 seconds.
Any clues that I described that makes you know what is going on?

Great that gives me a big clue, which asc file do you think I need to look in?
/mnt/applications/livepkgr/main.asc
/mnt/applications/multicast/main.asc
/mnt/applications/live/MemberClips/MemberClips.asc
/opt/adobe/fms/samples/applications/vod/main.asc
/opt/adobe/fms/samples/applications/livepkgr/main.asc
/opt/adobe/fms/samples/applications/multicast/main.asc
/opt/adobe/fms/samples/applications/live/main.asc
/opt/adobe/fms/scriptlib/framework.asc
/opt/adobe/fms/scriptlib/webservices/XMLSchema.asc
/opt/adobe/fms/scriptlib/webservices/SOAP.asc
/opt/adobe/fms/scriptlib/webservices/Namespace.asc
/opt/adobe/fms/scriptlib/webservices/ServiceManager.asc
/opt/adobe/fms/scriptlib/webservices/XMLSchemaDataTypes.asc
/opt/adobe/fms/scriptlib/webservices/Log.asc
/opt/adobe/fms/scriptlib/webservices/XMLUtil.asc
/opt/adobe/fms/scriptlib/webservices/SOAPConstants.asc
/opt/adobe/fms/scriptlib/webservices/WSDL.asc
/opt/adobe/fms/scriptlib/webservices/WebServicesClass.asc
/opt/adobe/fms/scriptlib/webservices/WSDLConstants.asc
/opt/adobe/fms/scriptlib/webservices/WebServices.asc
/opt/adobe/fms/scriptlib/webservices/XMLSchemaConstants.asc
/opt/adobe/fms/scriptlib/netservices.asc
/opt/adobe/fms/scriptlib/application.asc
/opt/adobe/fms/scriptlib/facade.asc
/opt/adobe/fms/applications/MemberClips/MemberClips.asc
/opt/adobe/fms/documentation/samples/livestreams/main.asc
/opt/adobe/fms/documentation/samples/StreamLength/main.asc
/opt/adobe/fms/documentation/samples/HelloWorld/HelloWorld.asc

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