Recorded FLV files contain corrupt timestamps

Howdy -
I'm running FMS 4.5.3 r2005 on standard AWS Linux box.  I'm recording the streams using NetStream.publish("appendWithGap") from a small custom Flash app running on IE+Windows.
Usually, the generated .flv file is fine. However, I've found a number of cases where the .flv file generated was corrupt.  By using ffprobe -show_packets I'm able to see that the presentation timestamp (PTS) of sequential packets occasionally remain the same.  This happens for both audio and video at times. For example, consider the output of the command:
$ ffprobe -show_packets saved.flv | egrep -e '(pts=|codec)'
codec_type=video
pts=0
codec_type=video
pts=0
codec_type=video
pts=0
codec_type=video
pts=0
codec_type=video
pts=0
codec_type=video
pts=0
codec_type=video
pts=3912
codec_type=video
pts=3944
codec_type=video
pts=3944
codec_type=video
pts=3944
codec_type=video
pts=3944
codec_type=video
pts=3944
codec_type=video
pts=3944
codec_type=video
pts=3944
codec_type=video
pts=3944
I really don't know much about the internals of the FLV format, but I assume that invalid timestamps like these make for a non-playable (corrupt) video.
Any idea what may cause FMS to record such a video?
What kind of information would be helpful to debug this?
Obviously, my client expects every video recorded to be one that an be played back, and so these corrupt videos are alarming to say the least.
FYI, due to privacy restrictions I can't share the recorded video without a signed NDA.  If it would help, I can provide the entire output of ffprobe.
Thanks,
Ben

Flvcheck has validated the format of file, and it is correct. The logs "Adding Silence message" indicates that audio message was expected and is not recieved after a particular time check, because of which video may appear stalled.
Flvcheck may claim the file is valid, but event after running flvcheck -s the video is corrupt.  According to ffprobe, many of the timestamps are still the same. When I attempt to play the file in an flv player, the entire video is run through up front in sort of a fast-forward view, and then the audio plays out more or less normally.
This makes sense, as the video player is probably playing all these frames with the same timestamp sequentially, which makes for the fast-forward effect.
To debug this issue, a good starting point would be, validating the input to FMS. FMS records what is published to it.
Does FMS tinker with the video frame timestamps, or are they just passed through to the file system?
Since you are able to reproduce this issue, can you please enable livestream logging and check if input stream to FMS is different from what it is recording.
Unfortunately I can't regularly reproduce it - though it does happen on a somewhat regular basis (it was happening a couple times a week).
Is it safe to turn live stream logging on for a few days to see if I can catch this issue happening? Or, will live logging chew up resources and cause issues?
Thanks for the assistance!
-Ben

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