It seems this has now been identified and fixed in Debian:
http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=448092

Will this fix automatically migrate to ubuntu?

** Bug watch added: Debian Bug tracker #448092
   http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=448092

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First char of some bzip2 files are changed by apt-cacher-ng
https://bugs.launchpad.net/bugs/234641
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