As noted on IRC the testcase was bogus. Attached is a proper testcase that also triggers the problem.
test_directories.tgz
Description: GNU Unix tar archive
diff -u -Nur test1/a/b/c/xyz test2/a/b/c/xyz --- test1/a/b/c/xyz 2010-02-03 16:21:37.769640266 +0100 +++ test2/a/b/c/xyz 2010-02-03 13:54:37.886386605 +0100 @@ -1 +1 @@ -2 +1
