Setting a preference to a global default simply removes it from database, so what you're seeing in response to php userOptions.php skin --usage is normal. Are you saying that users didn't observe a change in their preferences? (Note that user objects may be cached and although a change in prefrerences should result in cache invalidation, all kinds of glitches can happen).

Have you tried setting $wgDefaultSkin = 'vector'; yet?

akozak wrote:

We'd set the $wgDefaultSkin = 'vector', but are unable to replicate the original bug (the vector skin is enabled just fine according to our users). It's possible there was an unrelated issue (maybe a syntax error in LocalSettings when we first set the new default skin).

Is there somewhere in the documentation I or someone can make a note that "php userOptions.php skin --usage" will not display the skin preference if it's set to the default, since that's somewhat unintuitive behavior? Maybe it isn't that big of an issue.

Thanks for the help!

syntax error in LocalSettings

...always result in wiki being completely unusable.

Is there somewhere in the documentation

That's bug 1 :/