I believe that's an issue with library path ordering. That looks like you have a newer "released" version of FFmpeg installed on your system. This started to happen after ffmpeg made 0.5+ releases.
I'm not sure when I addressed this or if it corrects your situtation, but I'll take a look this weekend.
I'd check for libavformat/libavfilter/libavcodec/libswscale libraries in your lib/ directories. If they are there, try disabling them temporarily and building again.
corey