H.264 Transcoding and missing video

[ougryphon]

I'm using VLC 2.0.5 to transcode some .flv files into a format such as .mp4 or .mkv so I can play them off a flash drive on my TV. The flv files already contain h.264 video and MP4A/AAC audio, so really all I need to do is remux them with either the MP4 or MKV muxer. I've tried this both with the GUI and from the command line. The command line (from Windoze) is below:

vlc -I dummy myfile.flv --sout#transcode{}:standard{access="file",mux="mp4",dst="C:\myfile.mp4"}

The transcode works fine except the resulting video is missing the first 3-10 seconds of video. To be clear, the file plays with just sound but no video for the first few seconds, and then the video appears. The video, when it starts, is synched with the audio. I get the same result with both MKV and MP4 muxers. I've also tried transcoding from H.264 to H.264 (no scaling) and instead of missing video I get corrupted video (appears to be excessive gamma) for the same time period (3-10s) followed by good video.
I've had this problem on a lot of files and on multiple computers - one was XP and the other was Windows 7. I imagine I'm not the only person having this problem, but I couldn't find anything similar when I searched the forums (my search-fu is weak, apparently). Is there another way to do what I'm trying to do - basically remuxing the streams with a new wrapper? Is there a known workaround for this kind of thing or am I missing something obvious? Your help is appreciated.