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(Paying customer) Does not work with Quicktime recordings from OS X 10.8

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I've been quite happy with ffmpegX, as it has been essential for me for cropping videos, so I have donated to show my appreciation. However I am currently running into a show-stopper. I previously had been recording my screen in OS X 10.6 with quicktime, and then cropping with ffmpegX. But I find that the screen recordings that are made by Quicktime from OS X 10.8 cannot be processed! As in, the processing comes up, and immediately completes yielding a 0 byte file. This happens whether I am running ffmpegX from 10.8 or my old known-to-work copy from 10.6.

Please help with this as I have probably 50 hours of screen recordings I had recorded before I realized this error was happening. (I can provide a small 1MB file that shows this error in practice.)

Thanks

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Example info from the progress app for a file that was recorded with Quicktime on 10.8 (broken):

FFmpeg version CVS, Copyright (c) 2000-2004 Fabrice Bellard
Mac OSX universal build for ffmpegX
libavutil version: 49.0.0
libavcodec version: 51.9.0
libavformat version: 50.4.0
Sun Apr 28 14:57:43 EDT 2013
[mov,mp4,m4a,3gp,3g2,mj2 @ 0x5597b8]negative ctts, ignoring
Seems that stream 1 comes from film source: 50000.00 (50000/1) -> 30.00 (30/1)
Input #0, mov,mp4,m4a,3gp,3g2,mj2, from '/Volumes/M/1/Day2-raw/test.mov':
Duration: 00:00:06.5, start: 0.000000, bitrate: 1560 kb/s
Stream #0.0(und): Audio: aac, 44100 Hz, stereo
Stream #0.1(und), 30.00 fps(r): Video: h264, yuv420p, 1440x900
Codec type mismatch for mapping #0.0 -> #0.0


Example info from the progress app for a file that was recorded with Quicktime on 10.6 (working):
FFmpeg version CVS, Copyright (c) 2000-2004 Fabrice Bellard
Mac OSX universal build for ffmpegX
libavutil version: 49.0.0
libavcodec version: 51.9.0
libavformat version: 50.4.0
Sun Apr 28 15:17:58 EDT 2013
[mov,mp4,m4a,3gp,3g2,mj2 @ 0x5597b8]negative ctts, ignoring
Input #0, mov,mp4,m4a,3gp,3g2,mj2, from '/Volumes/M/2/Day2-Raw/test.mov':
Duration: 00:00:08.1, start: 0.000000, bitrate: 1548 kb/s
Stream #0.0(und), 15.00 fps(r): Video: h264, yuv420p, 1440x900
Stream #0.1(und): Audio: aac, 44100 Hz, stereo
Output #0, mp4, to '/Volumes/M/2/Day2-Raw/test.mov.ff.mp4':
Stream #0.0, 15.00 fps(c): Video: mpeg4, yuv420p, 1440x900, q=2-9, 7909 kb/s
Stream #0.1: Audio: aac, 48000 Hz, stereo, 96 kb/s
Stream mapping:
Stream #0.0 -> #0.0
Stream #0.1 -> #0.1
video:2992kB audio:58kB global headers:0kB muxing overhead 28.458613%
bench: utime=2.312s
Encoding completed on Sun Apr 28 15:18:00 EDT 2013

Is the issue that 10.8 seems to record in H264 by default and 10.6 recorded in mpeg4 by default?

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