You could put the following in a script and run it out of cron. It would need commands added to move the files once they're processed. I've just copy/pasted from a script of mine, so you'll also need to modify the mencoder options:
Code:
for i in *flv;
do
ORIGINAL=`basename $i .flv`
NEWNAME=${ORIGINAL}.mpg
/usr/bin/mencoder -oac lavc -ovc lavc -of mpeg -mpegopts format=dvd:tsaf \
-vf scale=720:576,harddup -srate 48000 -af lavcresample=48000 \
-lavcopts vcodec=mpeg2video:vrc_buf_size=1835:vrc_maxrate=9800:vbitrate=5000:keyint=15:trell:mbd=2:precmp=2:
subcmp=2:cmp=2:dia=-10:predia=-10:cbp:mv0:dc=10:vstrict=0:acodec=ac3:abitrate=192:aspect=4/3 \
-ofps 25 -o $NEWNAME $i
done