A new version v1.3.7 was recently released that fixed a number of issues. Can you try upgrading to the new version and then seeing if you experience the same issue?
I've not experienced this myself. When I upload a theme I upload a zip file with the directory name "foo", and after my auto-updates the directory name stays the same.
I do know the kind of thing you're talking about, though, because if I download a theme directly from Github, it has the folder/directory name of "danyork-foo-hash". However, I've not seen that renaming behavior after an auto-update.