Going through the code I figured out the problem that is  that is causing save 
to fail when set to "All documents"--a classic Python bug.
If an item is deleted from a list while that list is being looped through, then 
it's like sawing off the branch of a tree you are sitting on. Here is the code:

    for i in range(len(docs)):
      doc = docs[i]
      ...
      docs.remove(doc)

The code will break with 'list index out of range' if a list member is
deleted.

There is a simple fix--just reverse the direction of the loop:

    for i in reversed(range(len(docs))):

I have submitted a patch that fixes both errors. Please head over to 
https://bugzilla.gnome.org/show_bug.cgi?id=659437
and mark the bug "confirmed" if you are getting the error described in this bug 
report.

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https://bugs.launchpad.net/bugs/1244338

Title:
  External tool won't run if "Save" is set to "All documents"

Status in “gedit” package in Ubuntu:
  Confirmed

Bug description:
  Since upgrading to Ubuntu 13.10/gedit 3.8.3 external tools won't be
  run if the "Save" option is set to "All documents". If the setting it
  to "None" or "Current documents" then the tool will run again.

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