I've had this bug for awhile, I thought it was just me breaking things as I learn. But here goes, maybe someone else can check on their Buddypress + Pagelines install.
Go to your groups page and then the second page of that list if you have one. There are no "Join Group" buttons on the second sheet of groups in the directory. They show up on the first sheet then disappear after that. If you go back to the first page, they are there again.