git diff vs git diff-files

I have a billion testsuite golden output files that have changed due
to an explicit ordering of objects I've imposed on output. A helper
script I wrote to help parse the diffs (to ignore order-only
differences) noticed that one hunk had a different number of additions
and deletions. I'm manually copying and pasting the hunks from git add
-i into the script. However, when I used git diff to get at the
changes, to discover which line was the offending one, all additions
and deletions were exactly matched!

With strace I noticed that git add -i calls git diff-files, and that's
about as far as I can conveniently trace where things are going weird.
Weird:

$ /usr/local/git/bin/git diff-files -p --color -- TwoStageAmp-output.net

diff --git a/gnetlist/tests/common/outputs/osmond/TwoStageAmp-output.net

b/gnetlist/tests/common/outputs/osmond/TwoStageAmp-output.net
index a5ee1e7..a9f3620 100644

--- a/gnetlist/tests/common/outputs/osmond/TwoStageAmp-output.net
+++ b/gnetlist/tests/common/outputs/osmond/TwoStageAmp-output.net

@@ -1,47 +1,47 @@
-Part unknown { Name Cout }
-Part unknown { Name R5 }
-Part unknown { Name R4 }
-Part unknown { Name RE2 }
-Part unknown { Name Q2 }
+Part unknown { Name R8 }
 Part unknown { Name A3 }
-Part unknown { Name R3 }
 Part unknown { Name A2 }
-Part unknown { Name RE1 }
 Part unknown { Name A1 }

[snip]

$ /usr/local/git/bin/git diff TwoStageAmp-output.netdiff --git
a/gnetlist/tests/common/outputs/osmond/TwoStageAmp-output.net
b/gnetlist/tests/common/outputs/osmond/TwoStageAmp-output.n
index a5ee1e7..a9f3620 100644

--- a/gnetlist/tests/common/outputs/osmond/TwoStageAmp-output.net
+++ b/gnetlist/tests/common/outputs/osmond/TwoStageAmp-output.net

@@ -1,47 +1,47 @@
-Part unknown { Name Cout }
-Part unknown { Name R5 }
-Part unknown { Name R4 }
-Part unknown { Name RE2 }
-Part unknown { Name Q2 }
+Part unknown { Name R8 }
 Part unknown { Name A3 }
-Part unknown { Name R3 }
 Part unknown { Name A2 }
-Part unknown { Name RE1 }
-Part unknown { Name Q1 }  <--- Not present with diff-files output
 Part unknown { Name A1 }

[snip]

The index is clean on TwoStageAmp-output.net (but by now a million
other files are dirty in the index). While I discovered this issue
with Ubuntu's 1.7.1, I got the same behaviour with git
1.7.12.rc2.18.g61b472e

What's going on here? I'll leave my tree in whatever weird state it
might be, for a while, in case anyone wants me to try various things.
At this point I want to understand what's going on, in case there's
either a learning moment for me or a bug, rather than just finding a
workaround.