ifupdown itself doesn't have any function to edit the interfaces file,
so it's not an ifupdown bug.

If you have NetworkManager installed, that may indeed be the problem, NM
is never supposed to touch /etc/network/interfaces but I honestly can't
remember its behaviour on 8.04.

Could you try with 10.04 and if it still happens, file a bug against NM?

** Changed in: ifupdown (Ubuntu)
       Status: New => Invalid

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https://bugs.launchpad.net/bugs/416562

Title:
  Bonding configuration in /etc/network/interfaces is altered by unknown
  process

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