Have you tried it putting the glossary on the front page as suggested in the docs - you can add it to the main menu and hide the main menu. Is glossary autolinking enabled everywhere? Have you tried adding a new term in a course and not seeing the auto-linking - or did you just look at terms already created? (I ask because sometimes when I make a glossary it doesn't immediately link words I already had, but it does link new ones I add afterwards)
When you say you were hoping the words in the glossary would link to Moodle books/Articulate courses , did you mean these books were part of the glossary description? Would the activity names auto-linking filter work any better?