First, we need to fix ffmpeg for Ubuntu. We'll build it from source...but don't worry, it won't hurt. We'll also need to install some other libraries. So, here goes:

sudo apt-get build-dep ffmpeg
sudo apt-get install liblame-dev libfaad2-dev libfaac-dev libxvidcore4-dev liba52-0.7.4 liba52-0.7.4-dev
apt-get source ffmpeg
cd ffmpeg-*/
./configure --enable-gpl --enable-pp --enable-vorbis \
	--enable-libogg --enable-a52 --enable-dts \
	--enable-dc1394 --enable-libgsm --disable-debug --enable-mp3lame \
	--enable-faad --enable-faac --enable-xvid --enable-pthreads --enable-x264
make
sudo checkinstall -D make install

It will go through a bunch of stuff and prompt you on the last command for a few things. First, hit y to create docs, then just hit enter at the EOF question. Next, it will take you to the name and version. Edit #2 (name) to be ffmpeg, then edit #3 (version) to be something newer than what it is...so, either 1.cvsxxxxxx or some other way. I had a bit of trouble with this step, so I simply did a sudo make install instead of the whole checkinstall. If you don't mind not having a dpkg for it, then I'd recommend going straight to a sudo make install. Now, ffmpeg is fixed, time to move onto gtkpod's abilities.