Summary
H.264 video seems to have a really high frame rate that requires a scaling factor to the applied to the duration of video that I'm trying to extract (900x lower).

Body
I'm trying to extract a clip from a movie that I have in MP4 format (created using Handbrake). After trying mencoder and VLC, I decided to give FFmpeg a shot since it was the least troublesome when it came to copying the codecs. That is, compared to mencoder and VLC, the resulting file was still playable in QuickTime (I know about Perian, etc, I'm just trying to learn how all this works).

Anyway, my command was as follows:

ffmpeg -ss 01:15:51 -t 00:05:59 -i outofsight.mp4 \ 
-acodec copy -vcodec copy clip.mp4

During the copy, The following comes up:

Seems stream 0 codec frame rate differs from container frame rate: 45000.00 (45000/1) -> 25.00 (25/1)
Input #0, mov,mp4,m4a,3gp,3g2,mj2, from outofsight.mp4':
  Duration: 01:57:42.10, start: 0.000000, bitrate: 830 kb/s
    Stream #0.0(und): Video: h264, yuv420p, 720x384, 25 tbr, 22500 tbn, 45k tbc
    Stream #0.1(eng): Audio: aac, 48000 Hz, stereo, s16
Output #0, mp4, to 'out.mp4':
    Stream #0.0(und): Video: libx264, yuv420p, 720x384, q=2-31, 90k tbn, 22500 tbc
    Stream #0.1(eng): Audio: libfaac, 48000 Hz, stereo, s16
Stream mapping:
  Stream #0.0 -> #0.0
  Stream #0.1 -> #0.1
Press [q] to stop encoding
frame= 2591 fps=2349 q=-1.0 size=    8144kB time=101.60 bitrate= 656.7kbits/s
…

Instead of a 5:59 duration clip, I get the entire rest of the movie. So, to test this, I ran the ffmpeg command with -t 00:00:01. What I got was exactly a 15:00 minute clip. So I did some black box engineering and decided to scale my -t option by calculating what value to enter given that 1 second was interpreted as 900 s. For my desired 359 s clip, I calculated 0.399 s and so my ffmpeg command became:

ffmpeg -ss 01:15.51 -t 00:00:00.399 -i outofsight.mp4 \ 
-acodec copy -vcodec copy clip.mp4

This works, but I have no idea why the duration is scaled by 900. Investigating further, each ffmpeg run has the line:

Seems stream 0 codec frame rate differs from container frame rate: 45000.00 (45000/1) -> 25.00 (25/1)

45000/25 = 1800. Must be a relation somewhere. Somehow, the obscenely high frame rate is causing issues with the timing. How is that frame rate so high? The best part about this is that the resulting clip.mp4 has the exact same feature (due to the copied video codec), and taking further clips from this needs the same scaling for the -t duration option. Therefore, I've made it available for anyone willing to check this out.

Appendix
The preamble for ffmpeg on my system (built using MacPorts ffmpeg port):

FFmpeg version 0.5, Copyright (c) 2000-2009 Fabrice Bellard, et al.
  configuration: --prefix=/opt/local --disable-vhook --enable-gpl --enable-postproc --enable-swscale --enable-avfilter --enable-avfilter-lavf --enable-libmp3lame --enable-libvorbis --enable-libtheora --enable-libdirac --enable-libschroedinger --enable-libfaac --enable-libfaad --enable-libxvid --enable-libx264 --mandir=/opt/local/share/man --enable-shared --enable-pthreads --cc=/usr/bin/gcc-4.2 --arch=x86_64
  libavutil     49.15. 0 / 49.15. 0
  libavcodec    52.20. 0 / 52.20. 0
  libavformat   52.31. 0 / 52.31. 0
  libavdevice   52. 1. 0 / 52. 1. 0
  libavfilter    1. 4. 0 /  1. 4. 0
  libswscale     1. 7. 1 /  1. 7. 1
  libpostproc   51. 2. 0 / 51. 2. 0
  built on Jan  4 2010 21:51:51, gcc: 4.2.1 (Apple Inc. build 5646) (dot 1)

EDIT
Not sure whether it was a bug or not, but it seems to be fixed now in my current version of ffmpeg, at least for this video (version 0.6.1 from MacPorts).