You certainly have solved your problem by now, but in case others come across this thread, I just did the following on Ubuntu 12.04 LTS:
Make sure you have the necessary tools installed:
sudo apt-get install build-essential yasm
After downloading the latest source of ffmbc, and unpacking it into ~/src/
cd ~/src/FFmbc-0.7-rc7
./configure --enable-gpl --enable-nonfree --enable-runtime-cpudetect
make
sudo make install
make gave out lots of warnings, but it seems to work fine anyway.