I tried to use the CommonsHelper (http://tools.wmflabs.org/commonshelper/), but instead of directing me to the OAuth page, a window popped up with the message "Auth not OK". I could not get past that stage.
Assuming you are logged in on mediawiki.org, what is the exact full message you get?
Do you end up on https://www.mediawiki.org/w/index.php?title=Special:OAuth/authorize (with some URL parameters included)?
Yes, I was logged in on mediawiki.org. No, the usual OAuth window asking me to authorize did not appear.
The only thing that happened was that a window with the message "Auth not OK" popped up.
This has happened to me several times as well recently. At my home computer, I literally cannot use CommonsHelper anymore, and have been unable to for months. Oddly, when I swapped to a different computer temporarily, it worked for a brief period of time before again popping the "Auth not OK" message and not allowing me to re-authenticate.