To convert an MKV to AVI, I do two things. The first thing I do is this:

ffmpeg -i filename.mkv -vcodec copy -acodec copy output.avi

This converts the MKV to an AVI, but the problem is that the video does not play smoothly for some reason. That's fine, because if I do one more thing it gets fixed:

ffmpeg -i output.avi -vcodec mpeg4 -b 4000k -acodec mp2 -ab 320k converted.avi

After I do this then the file plays without problem. I had success doing it this way for one file, but then I tried it on another file, and there is a slight, but noticeable loss in video quality. This is the output I get when doing the second step:

FFmpeg version 0.6.1, Copyright (c) 2000-2010 the FFmpeg developers
  built on Dec 29 2010 18:02:10 with gcc 4.2.1 (Apple Inc. build 5664)
  configuration: 
  libavutil     50.15. 1 / 50.15. 1
  libavcodec    52.72. 2 / 52.72. 2
  libavformat   52.64. 2 / 52.64. 2
  libavdevice   52. 2. 0 / 52. 2. 0
  libswscale     0.11. 0 /  0.11. 0

Seems stream 0 codec frame rate differs from container frame rate: 359.00 (359/1) -> 29.92 (359/12)
Input #0, avi, from 'output.avi':
  Metadata:
    ISFT            : Lavf52.64.2
  Duration: 00:04:17.21, start: 0.000000, bitrate: 3074 kb/s
    Stream #0.0: Video: mpeg4, yuv420p, 704x480 [PAR 229:189 DAR 5038:2835], 29.92 fps, 29.92 tbr, 29.92 tbn, 359 tbc
    Stream #0.1: Audio: vorbis, 48000 Hz, stereo, s16
Output #0, avi, to 'nidome_no_kanojo.avi':
  Metadata:
    ISFT            : Lavf52.64.2
    Stream #0.0: Video: mpeg4, yuv420p, 704x480 [PAR 229:189 DAR 5038:2835], q=2-31, 4000 kb/s, 29.92 tbn, 29.92 tbc
    Stream #0.1: Audio: mp2, 48000 Hz, stereo, s16, 320 kb/s
Stream mapping:
  Stream #0.0 -> #0.0
  Stream #0.1 -> #0.1

I just used arbitrarily large settings on the second step and it worked nicely before but not in this case. What settings should I use?