How did you configure Clearspace to use your custom AuthFactory? A build property? A Jive property? Do you see any error messages in your logs?
You might try turning on the debug logs via the admin console --> system --> log viewer --> debug tab.
I configured ClearSpace to use a custom UserManager, GroupManager, and AuthFactory using the screen for that in the setup tool.
If there are other ways to specify those in a config file, I would be happy to try that -- can you give me some pointers?
For what it's worth, I just tried ClearspaceX 1.2 and I have the same behavior. During the first run when I go through the full setup wizard, the custom AuthFactory is loaded and single sign-on works. However after restarting the app server and going through the mini-setup-wizard (confirming home dir and license details), the custom AuthFactory is not loaded and single sign-on does not work.