git-ls-files prefix superset problem

I had been previously using git-1.1.3 on my local repositories
and I upgraded to the current git head:

b63fafdfd844c2037fba53b9944431c1378b4135

git commit stopped working, specifically it dies on
git-ls-files:

davem@sunset:~/src/GIT/net-2.6$ ../git/git-ls-files -- net/ipv4/tcp.c
fatal: git-ls-files: internal error - cache entry not superset of prefix
davem@sunset:~/src/GIT/net-2.6$ 

I added some debugging:

Trying get_pathspec([(null)],[net/ipv4/tcp.c])
prefixlen(0)
prefix_path() gives [net/ipv4/tcp.c]
ERROR: pathspec(net/ipv4/tcp.c)
verify_pathspec: len(9)
ERROR: len(9) ce_namelen(ce)(7) ce->name(COPYING)

Is something wrong with my index file?

I tried to rebuild it using:

git read-tree master
git checkout-index -f -a
git update-index --refresh

but I keep getting the same problem.

It happens on all of my local 2.6.x kernel GIT trees.

Any ideas?

Thanks a lot.