I took a look at the code of the Jack output module and with some
debugging and some luck i found the problem:

in modules/audio_output/jack.c on line 139:

aout_PacketInit is called with p_aout and this p_aout contains the wrong
sample rate, because it is set later, on line 146. Moving line 146 up
before the call to aout_PacketInit solved the problem.



** Attachment added: "diff"
   
https://bugs.launchpad.net/ubuntu/+source/vlc/+bug/987231/+attachment/3106995/+files/diff

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https://bugs.launchpad.net/bugs/987231

Title:
  VLC does not resample correctly with JACK

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