I have a similar problem - avi files with x264 video and aac audio
encoded using mencoder won't play back in totem (although they *do* play
in mplayer just fine)

[EMAIL PROTECTED]:~/tmp$ totem test.avi 
JACK tmpdir identified as [/dev/shm]
** Message: don't know how to handle audio/x-avi-unknown, codec_id=(int)28781
** Message: Missing plugin: gstreamer|0.10|totem|audio/x-avi-unknown 
decoder|decoder-audio/x-avi-unknown, codec_id=(int)28781 (audio/x-avi-unknown 
decoder)
no application found
** Message: No installation candidate for missing plugins found.
[EMAIL PROTECTED]:~/tmp$ mplayer test.avi 
MPlayer 2:1.0~rc1-0ubuntu13 (C) 2000-2006 MPlayer Team
CPU: Intel(R) Core(TM)2 CPU         T7600  @ 2.33GHz (Family: 6, Model: 15, 
Stepping: 6)
CPUflags:  MMX: 1 MMX2: 1 3DNow: 0 3DNow2: 0 SSE: 1 SSE2: 1
Compiled with runtime CPU detection.
Can't open joystick device /dev/input/js0: No such file or directory
Can't init input joystick
mplayer: could not connect to socket
mplayer: No such file or directory
Failed to open LIRC support. You will not be able to use your remote control.

Playing test.avi.
AVI file format detected.
VIDEO:  [h264]  720x416  24bpp  25.000 fps  750.0 kbps (91.5 kbyte/s)
Clip info:
 Software: MEncoder 2:1.0~rc1-0ubuntu13
xscreensaver_disable: Could not find XScreenSaver window.
GNOME screensaver disabled
==========================================================================
Opening video decoder: [ffmpeg] FFmpeg's libavcodec codec family
Selected video codec: [ffh264] vfm: ffmpeg (FFmpeg H.264)
==========================================================================
==========================================================================
Forced audio codec: mad
Opening audio decoder: [faad] AAC (MPEG2/4 Advanced Audio Coding)
AUDIO: 48000 Hz, 2 ch, s16le, 127.9 kbit/8.33% (ratio: 15986->192000)
Selected audio codec: [faad] afm: faad (FAAD AAC (MPEG-2/MPEG-4 Audio) decoder)
==========================================================================
AO: [alsa] 48000Hz 2ch s16le (2 bytes per sample)
Starting playback...
VDec: vo config request - 720 x 416 (preferred colorspace: Planar YV12)
VDec: using Planar YV12 as output csp (no 0)
Movie-Aspect is 2.46:1 - prescaling to correct movie aspect.
VO: [xv] 720x416 => 1024x416 Planar YV12 
GNOME screensaver enabled.116 ct: -0.030  62/ 62  5%  1%  0.7% 0 0 

Exiting... (Quit)


FWIW, m4a files play perfectly in rhythmbox.

Thanks.

-- 
aac encoder output not interoperable with aac decoder, possibly erroneous
https://bugs.launchpad.net/bugs/106322
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Bugs, which is the bug contact for Ubuntu.

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