I had exactly the same issue, on my new install using the blog as folder structure.
On the previous version using blog as sub domains structure, I did not have that issue.
To cure, I deleted the file on the server and uploaded it again. Nothing wrong with upload mode. RWX permissions were all identical.
BTW it says at top "themes can be enabled on a per blog basis". How?
Do you mean by site admin, or by user. Seems like user to me, and I would like it be admin.
Ditto for plugins on a per blog basis by admin.
UPDATE - above cured it once but is now not happy again. Can't correct it :-(