I had the same problem. My walk around was to use the raw-output of gnash.
The following bash script summarizes the single steps.
#!/bin/bash
SWFFILE=$1
MP4FILE=${SWFFILE%.*}.mp4
TMPFILE=/tmp/$(cat /dev/urandom | tr -dc 'a-zA-Z' | fold -w 32 | head -n 1).bin
TMPMP4=/tmp/$(cat /dev/urandom | tr -dc 'a-zA-Z' | fold -w 32 | head -n 1).mp4
# create raw-dump
GNASHCMD="dump-gnash -1 -r 1 -D $TMPFILE $SWFFILE"
OUTPUT="$(exec $GNASHCMD)"
# extract parameters
WIDTH="$(echo $OUTPUT | grep -o 'WIDTH=[^, }]*' | sed 's/^.*=//')"
HEIGHT="$(echo $OUTPUT | grep -o 'HEIGHT=[^, }]*' | sed 's/^.*=//')"
FPS="$(echo $OUTPUT | grep -o 'FPS_ACTUAL=[^, }]*' | sed 's/^.*=//')"
# create raw, uncompressed mp4 file
mplayer $TMPFILE -vo yuv4mpeg:file=$TMPMP4 -demuxer rawvideo -rawvideo fps=$FPS:w=$WIDTH:h=$HEIGHT:format=bgra
# create compressed mp4 (ffmpeg should work as well)
avconv -i $TMPMP4 $MP4FILE
# clean up
rm -rf $TMPFILE
rm -rf $TMPMP4