Okay, I investigated this a bit, and here's what I think is happening: pretty_print.py attempts to alphabetize just the affected-histogram elements, and tries to ignore the suffixes.  The way it does this is to keep the <suffix> elements in the same order relative to the <affected-histogram> element that follows them.  If <affected-histogram name="EmbeddedWorkerInstance.Start.StartMessageLatency"/> is inserted at the beginning of the <affected-histogram>s list, then everything works fine.  If it's inserted anywhere else, it ends up being sorted above the <suffix> elements.

This would be nice to fix -- by sorting all of the suffixes too -- but is a bit inconvenient given the current structure of the code.  Going to leave as available in case anyone wants to take a stab at it.

The following revision refers to this bug:
  https://chromium.googlesource.com/chromium/src.git/+/472a9d0d9e143632f9d096c589ae15caf820eb06

commit 472a9d0d9e143632f9d096c589ae15caf820eb06
Author: isherman <isherman@chromium.org>
Date: Mon Jul 03 22:03:09 2017

[Cleanup] Pretty-print histograms.xml

BUG= 737822 
TEST=none
R=asvitkine@chromium.org

Review-Url: https://codereview.chromium.org/2970573002
Cr-Commit-Position: refs/heads/master@{#484031}

[modify] https://crrev.com/472a9d0d9e143632f9d096c589ae15caf820eb06/tools/metrics/histograms/enums.xml
[modify] https://crrev.com/472a9d0d9e143632f9d096c589ae15caf820eb06/tools/metrics/histograms/histograms.xml

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I believe this is fixed now.