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One thing I forgot to mention was to hear pulseaudio-jack ensure you enable the JackSink audio module in Sound settings to hear pulseaudio.
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The scripts are attached at the bottom of this post.

They will enable all apps that use pulseaudio to still be about to play through pulseaudio is sinked with Jack.

Make sure you go to set up...

I too have just done a fresh install of Ubuntu 11.10 and needed to setup pulseaudio to run through JACK so this should help you too.

In the USC (Ubuntu Software Centre) type pulseaudio-module-jack...