I have had heaps of problems converting my .nuv MythTV files to other formats... I tried nuvexport, but it would segfault at some stage with mplayer or some library on my mythtv box. So I just figured out what nuvexport done, and it looks like it just spits out the nuv file raw to a fifo, where transcode or ffmpeg picks it up as raw and converts it.
Well this is the mythtranscode output for outputting to fifo, it outputs both audio and video
$ mythtranscode --showprogress -p autodetect -c 1022 -s 2005-07-02-21-10-00 -f /tmp/fifodir_16579/
Obviously u need to use the right parameters for your nuv file, this is something I found in nuvexport
So once you got that going just run transcode to pick up from that fifo in raw format! ta da
$ transcode -V --print_status 16 --import_asr 2 -k -i /tmp/fifodir_16579/vidout \ -p /tmp/fifodir_16579/audout -H 0 -x raw -g 720x576 -f 25,3 -n 0x1 -e 48000,16,2 \ -j 12,14,12,14 -y xvid -Z 624x464 -N 0x55 -b 128,0,2,0 -R 1,/tmp/xvid.16579.log -w960 -o ~/test.avi
If you want to know what all the options are for transcode, I found this website
I've never successfuly been able to convert a (mythtv) .nuv file directly to something else, so bah, this works for the time being