Main / secundary glossary doesn't influence autolinking. To make a glossary global check the global option (see screenshot)
I don't know why autolinking doesn't start. You have set the autolink option when adding an entry, right? Have you set autolinking to YES? (see screenshot)
BTW clicking on the question mark icon next to an option shows help for that option.
As a last resort: go to http://yourserver/yourmoodle/admin/filters.php and
make sure glossary autolinking is active
lower the text cache lifesize to see immediate results (put it to a higher value after testing)
