I get this error message on WP 3.5.1:
ERROR: This authors page base is already used somewhere else (for a custom post type archive page). Please choose another one.
I tried multiple times and even entered totally random strings.
The author slug part works though.
I do not see any WP_DEBUG errors.
When I deactivated most other plugins, I could then get it to save the Permalinks settings, but when I tried to visit a particular author's URL, it resulted in a 404 when the author Permalinks were saved and not a 404 before I saved the custom author Permalinks.
Then it wouldn't let me set back to blank author Permalinks. It gave the above error message again.