Bug when encoding f4v videos longer than ~ 1 hour ?

Folks,
We're getting a strange problem with Adobe Media Encoder.
We encode a long (slightly more than 1 hour) f4v video
and Adobe Media Encoder reports that the file encoded
successfully with no errors. But when we scrub through
the video (i.e., move the play head from start to finish),
the video hangs early in the video.
The source video in original H.264 Quicktime format
works perfectly and is known to be OK. We have plenty
of disk space and memory, so that is not an issue.
We do not have this problem when encoding shorter f4v videos
(even slightly less than 1 hour). Does Adobe Media Encoder
have a bug when encoding f4v videos longer than about 1 hour?
Is there a workaround?
Thanks in advance,
Raja.

You can remove them from the iMovie timeline and replace(?) I believe iMovie plays the full quality video (there is an option on how iMovie previews the clips) but doesn't FCE play a lower resolution version? If you are not using the Highest Quality version in iMovie, what happens when the project is exported to Quicktime or iDVD? Does the video still studder?
Regards,

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