I launch BE by opening my default database, that means I have my database in the dock, not BE. This way, BE opens always with my default database (hope this was clear enough)
I launch bookends by clicking on the "go to bookends" button from within word. When I do this, it opens the program, but I have to manually open a database. There is no database open automatically.
When I click "Go to Bookends" Bookends launches and opens the last-opened database. Try removing Bookends 9 Preferences and relaunching Bookends (you'll need your serial number handy) and see if that restores this for you.