I'm having the same problem. I created a bug MDL-58022 in the tracker, and also attempted to fix the bug, but without success.
See https://github.com/ecampbell/moodle/blob/MDL-58022/mod/book/settings.php for my revised code.
I have a Book plugin at https://github.com/ecampbell/moodle-booktool_wordimport which is supposed to include custom settings code, but I'm not sure where the problem is. In any event, I don't see what I expect, which is a link to a settings page in a column to the right of the plugin name in the Plugins Overview page.
If you can spot any obvious coding errors, please let me know.