I am trying to convert movies playable by mplayer to flash by using avi2swf.
This works ok, but the resulting movies have strange rhytmically increasing palette distortions, that pop to normal all few seconds and then increase again.

The palette distortion were gone, when I use transcode instead of mplayer before avi2swf like this:
1. Step: transcode -i in.avi -x mplayer,mplayer -o out.avi -y ffmpeg,pcm -F mpeg4 -w 1000
2. Step: avi2swf -x out.avi -o movie.swf

Normally I use this before avi2swf:
mencoder in.avi -o out.avi -oac pcm -ovc lavc -vf scale=320:240
Then I get audio, but the above mentioned palette distortions.

I would like is this error that appears from avi2swf to disappear:
Converting frame 6 : Cannot convert non-YUV image to BGR24

The transcode output looks like this:
nyk@izbrio ~ $ transcode -i /tmp/nic4.avi -x mplayer,mplayer -o out.avi -y ffmpeg,pcm -F mpeg4 -w 1000
transcode v0.6.14 (C) 2001-2003 Thomas Oestreich, 2003-2004 T. Bitterberg
[transcode] (probe) suggested AV correction -D 0 (0 ms) | AV 0 ms | 0 ms
[transcode] auto-probing source /tmp/nic4.avi (ok)
[transcode] V: import format | DivX5 RIFF data, AVI (V=mplayer|A=mplayer)
[transcode] V: import frame | 720x480 1.50:1
[transcode] V: bits/pixel | 0.097 (low)
[transcode] V: decoding fps,frc | 29.970,4
[transcode] V: Y'CbCr | YV12/I420
[transcode] A: import format | 0x11 unknown [44100, 4,2] 355 kbps
[transcode] A: export format | 0x55 MPEG layer-3 [44100, 4,2] 128 kbps
[transcode] V: encoding fps,frc | 29.970,4
[transcode] A: bytes per frame | 0 (0.000000)
[transcode] A: adjustment | 0@1000
tc_memcpy: using libc for memcpy
[transcode] V: video buffer | 10 @ 720x480
[import_mplayer.so] v0.0.5 (2003-03-10) (video) rendered by mplayer | (audio) rendered by mplayer
[export_pcm.so] v0.0.4 (2003-09-30) (audio) PCM (non-interleaved)
[export_ffmpeg.so] v0.3.13 (2004-08-03) (video) FFmpeg0.4.9-pre1b4743 | (audio) MPEG/AC3/PCM
[import_mplayer.so] mplayer -hardframedrop -vo null -ao pcm -nowaveheader -aofile /tmp/mplayer2transcode-audio.VNDhfj "/tmp/nic4.avi" > /dev/null 2>&1
[import_mplayer.so] mplayer -benchmark -noframedrop -nosound -vo yuv4mpeg "/tmp/nic4.avi" -osdlevel 0 > /dev/null 2>&1
[import_mplayer.so] tcextract -i ./stream.yuv -x yv12 -t yuv4mpeg
tc_memcpy: using libc for memcpy
[export_ffmpeg.so] Using FFMPEG codec 'mpeg4' (FourCC 'DIVX', MPEG4 compliant video).
[export_ffmpeg.so]: WARNING: Interlacing parameters unknown, use --encode_fields
[export_ffmpeg.so]: INFO: No profile selected
[export_ffmpeg.so] Neither './ffmpeg.cfg' nor '~/.transcode/ffmpeg.cfg'
[export_ffmpeg.so] found. Default settings will be used instead.
[export_ffmpeg.so]: INFO: Starting 1 thread(s)
[export_ffmpeg.so]: INFO: Set display aspect ratio to input
encoding frames [000000-000566], 83.78 fps, EMT: 0:00:18, ( 0| 0| 0)
clean up | frame threads | unload modules | cancel signal | internal threads |sh: line 1: 2556 Broken pipe mplayer -hardframedrop -vo null -ao pcm -nowaveheader -aofile /tmp/mplayer2transcode-audio.VNDhfj "/tmp/nic4.avi" >/dev/null 2>&1
done
[transcode] encoded 567 frames (0 dropped, 0 cloned), clip length 18.92 s

When I don't put the -x mplayer option, I get this error:
[transcode] warning : [import_ffmpeg.so] Unsupported decoded frame format: 16

delete this... but how?

I advise you to try video to flash converter by geovid. It converts video to flash without any quality losses.Its quite nice programm & easy to manage.You will have Full control over the converted Flash Video: video quality, frame rate, size, duration and other parameters. You do not need any special programs or plugins to create SWF video file, simple select and convert Video to swf Flash file. You can get the app from:http://www.geovid.com/Video_to_Flash_Converter/