is there any possibility to generate .mkv files out from ffmpegx and not .mp4 files when encoding with h264? I reckon mkv would be the better solution...
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You may use ffmpegx for compression and get the xxx.mp4 into mkvtoolnix for configuring your mkv yourself. mkvtoolnix accept mp4.
ffmpegx is likely to compress x264.
Handbrake has some errors with determinates mkv when converts mkv to mkv or mp4.
ffmpegx has the posibility (with x264) to change the profile to 4.1
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