Hit and miss editing and playing mp4

Hello,

I've been trying to play (and also cut) mp4 videos I downloaded from the cspan website.

I tried these players-

mplayer - skips around. audio not synched. will tend to loop a bit of content and not play most of the video.
vlc - plays ok, but frequent, small hangs (every 15-20sec there will be a hiccup) in video.
openshot - plays perfectly only if you right click the clip in the project files box and choose 'Preview file' - if you try to play or scroll the clip in the 'Video Preview' window it will hang and not play.

I used these commands to cut out a portion of the mp4 -

ffmpeg -i file.mp4 -acodec copy -vcodec copy -f mov file.mov
ffmpeg -i file.mov -ss 00:10:00 -t 00:01:00 -vcodec copy -acodec copy filecut.mov

When playing the chopped video, the same problems persist (and the hangs happen at the exact same places when using the same player). The chopped video plays on openshot preview like the source video did above, but the audio is no longer synced.

All I want to do is to make playable cuts of the original mp4 files. They will eventually be in flv format, fairly low quality for web streaming. I cannot even tell whether the cut video is good or not, since the players all choke on it.

So the goal is:
1- convert mp4 to a format I can edit
2- chop out a few minutes of video
3- convert video to flv format for web streaming.

This is on i7-3610qm w/ lotsa ram.

$ uname -r
3.8.9-200.fc18.x86_64

Thanks for help,
-b