strange histories from filter-branch

I tried sending this mail to the "git for humans" mailing list but got no response, so I'll try here.

I've been running the git filter-branch described on this page:

http://stackoverflow.com/questions/14759345/how-to-split-a-git-repository-and-follow-directory-renames.

But the resulting history includes at least two extraneous commits, i.e., commits that appear to affect no files in the subdirectory of interest. (The corresponding commits in the original history do affect files, but those files are in another subdirectory.)

I also noticed several "duplicate parent" errors during the git filter-branch. The page http://stackoverflow.com/questions/15161809/git-duplicate-parent-causes-half-the-history-to-to-disappear says that those errors can produce an incomplete new history, so I'm now wondering if, in addition to including extraneous commits, my new history might also be missing some. Both that page and http://stackoverflow.com/questions/7489713/git-duplicate-parent/7501703#7501703 say that the "duplicate parent" errors should disappear if "git filter-branch" is first run with no filter. But that didn't work for me.

Any ideas?