Repository module code completely different from downloaded file
I think the master branch is still pointing to an old (probably obsolete) branch. To get the latest version, which is inline with the zip file you downloaded, you should use:

git clone --branch 7.x-2.x http://git.drupal.org/project/soundmanager2.git

Maybe you should open an issue and point them to the Moving from a master to a major version branch documentation.