Error first sec due to wrong streams?

[simchippy]

I am converting a number of .mkv files and a few are crashing with the following error.
When I compare them to the mkv files that convert in VLC, I noticed the streams are reversed.
Both play fine with VLC

Successful mkv conversion:
Stream 0 is AC1 Video
Stream 1 is A52 Audio

Crashing mkv:
Stream 0 is A52 Audio
Stream 1 is AC1 Video

with the following error:
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 Aug 3 20:06:29 EDT 2008
[matroska @ 0x5597b8]Ignoring seekhead entry for ID=0x1549a966
[matroska @ 0x5597b8]Ignoring seekhead entry for ID=0x1654ae6b
[matroska @ 0x5597b8]Ignoring seekhead entry for ID=0x114d9b74
[matroska @ 0x5597b8]Unknown entry 0x73a4 in info header
[matroska @ 0x5597b8]Unknown track header entry 0x55aa - ignoring
[matroska @ 0x5597b8]Unknown track header entry 0x23314f - ignoring
[matroska @ 0x5597b8]Unknown track header entry 0x55ee - ignoring
[matroska @ 0x5597b8]Unknown track header entry 0xaa - ignoring
[matroska @ 0x5597b8]Unknown track header entry 0x55aa - ignoring
[matroska @ 0x5597b8]Unknown track header entry 0x23314f - ignoring
[matroska @ 0x5597b8]Unknown track header entry 0x55ee - ignoring
[matroska @ 0x5597b8]Unknown track header entry 0xaa - ignoring
Seems that stream 1 comes from film source: 1000.00 (1000000000/1000000) -> 0.08 (1/12)
Input #0, matroska, from '/Users/Tom/Downloads/NewsBin/alt.binaries.multimedia/swingtown.101.720p-dimension/ST.S01E03.mkv':
Duration: 00:42:28.7, bitrate: N/A
Stream #0.0: Audio: ac3, 48000 Hz, 5:1
Stream #0.1, 0.08 fps(r): Video: h264, yuv420p, 1280x720
Codec type mismatch for mapping #0.0 -> #0.0


Is there any way to fix this with ffmpegX or another app?

Thanks

[Case]

Codec type mismatch for mapping #0.0 -> #0.0

Your source file has the audio stream (#0.0) mapped before the video stream (#0.1). This is reverse from what the ffmpeg engine expects. You may fix this "Codec type mismatch for mapping"-error by indicating that the streams are reversed. To do so, check the "Invert mapping" checkbox in the Audio tab.