As you may have figured, I work with WordPress MU a lot. Like every day a lot. I also work with themes a lot. (Don’t ask how many are on my local install to play with. I could host my own repository.)
My normal work flow is to upload a zipped theme to the themes directory and unpack it on the server. It’s just faster for me, and works fine and dandy. Every so often, twice now, I’d find a theme that just would not show up in the Site Admin->Themes menu no matter what I tried. Even the same theme on different installs. It would work locally for me or in single WordPress installs, and other people said the same themes worked on their WPMU installs.
It was like it wasn’t working just for me, to spite me. Usually something like this is User Error, but I even got people (*cough* Ron *cough*) to check my work.
Today I *finally* figured it out – it was a permissions issue! For some reason all the themes’ files were set to 444. When I set them to 644, it suddenly showed up in the themes list.
Weird. I haven’t looked at the code yet, but I will and if there’s a check in there I’ll file a ticket. 🙂 Because that was driving me nuts.