filter-branch --subdirectory-filter prematurely truncating history?

I'd like to spin a subdirectory of an existing git repo off in to its own repo while preserving history. From what I've read, I should be able to do this with a fresh clone followed by git filter-branch --subdirectory-filter MYSUBDIR, assuming I don't care about other branches or tags. This runs, and when it's done, I have a repo that contains the subdir's contents as its root. So far so good.

I would expect to see the subdir's full history when I run git log, but instead it cuts off prematurely, showing the first commit to be some relatively recent minor change I'll call FOO. In gitk, I can see that history prior to FOO is still around, but FOO has no parents, and the commit before FOO has no children. In the original repo, FOO's parent was the merge of a branch which no longer exists, if this matters.

Am I expecting filter-branch to do something unreasonable? Is there an easy way to reconnect the orphaned history? Am I using the wrong tool for the job?