Check for tags you may have created that may keep the old tree from being garbage-collected.
Namely, git-filter-branch leaves tags on the original tree untouched and does not auto-move them to the new tree.
To get rid of it I did things like
git push . :refs/original/refs/tags/v1.0.x
git push origin :refs/original/refs/tags/v1.0.5
until all original and extra tags were gone