I'm having a similar issue, but it is when encoding to mp4 straight from
DVD. The temp files appear to get about 160 MB and then disappear. In
the end either the encoding hangs at ~96% or the encoding completes, but
either way no .mp4 file is created.

I think it stems from this:
[Option lavfopts: Unknown suboption 
i_certify_that_my_video_stream_does_not_use_b_frames
Error parsing option on the command line: -lavfopts
]

Why mencoder decided to error out on a previously acceptable option is a
bit of a stumper for me, but they decided to. This command line option
is hard-coded in k9copy.

I commented out:
libk9copy/k9mp4enc.cpp:286:                //*m_process << "-lavfopts" << 
"i_certify_that_my_video_stream_does_not_use_b_frames";
after reading the mplayer mailing list archives and compiled. 

That doesn't seem to work either. Now the encoder complains about the
possible issues surrounding the b frames and mplayer, which it
previously would not allow me to specify a command line argument for.

I am also now getting a problem in my compiled version that seems to prevent it 
from working:
$ k9copy 
QSettings: failed to open file '/etc/qt3/qt_plugins_3.3rc'
QComboBox::setCurrentItem: (cbInputDev) Index 0 out of range
KCrash: Application 'k9copy' crashing...
QSettings: failed to open file '/etc/qt3/qt_plugins_3.3rc'

So I'm not sure what I've got wrong there.

-- 
k9copy doesn't encode mpeg4
https://bugs.launchpad.net/bugs/228001
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