I've never had that problem. And I DO have that checkbox checked. To the best of my recollection, that's its default and is something I never changed. Maybe it's happening because you have it unchecked?
What I would do is check that box again, then tune in for a full hour broadcast and keep an eye on the autosave folder to see if that happens. Move any existing files out first, but let it do it's thing. It should decode all six files that are sent, then repeatedly overwrite each one as it decodes a repeat. HM01 sends each file 12 times in an hour (six in one half, six in the second), but at the end of that hour you should be left with just the six files that were transmitted.
Good luck!