Your first screenshot shows that you are using the FFmpeg from the Ubuntu repository, and not a compiled version that you would get from this guide. By default, FFmpeg from the Ubuntu repository does not have libx264 enabled. You must install libavcodec-extra-52 after installing FFmpeg if you want to enable libx264 and other restricted encoders. However, FFmpeg from the Karmic repository is troublesome because you can't encode to AAC audio (your WinFF preset uses AAC) with FFmpeg even after installing libavcodec-extra-52 because libfaac (the AAC encoder) has been removed due to a licensing issue. Annoying.
Anyway, in my opinion, the easiest way to get everything working right with FFmpeg and WinFF is to compile FFmpeg as shown in this guide, but maybe one of the WinFF developers will have some better advice since I do not have much experience with WinFF.
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