I'm experiencing the same bug here.
Now, seeing that a similar playback-pausing issue on mp3 to ogg transitions 
(lp: #921071) was fixed with a patched version of gst-plugins-base0.10 
(0.10.36-1ubuntu0.1):  "don't discard timestamps when consecutive input buffers 
have the same ts",  could it perhaps be, that a similar patch needs to be 
applied to the handling of flac files in gst-plugins-base0.10 ? 
Does anything stand out in the debug log?
Just guessing here.

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https://bugs.launchpad.net/bugs/1026678

Title:
  Playback stops when going from an ogg to a flac

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