I did a run within the last couple days with someone who had the same issue, but then picked up the quest requiring you to collect 5 runes; the run after picking up the quest had a rune in the chest. It seems if a quest is available to you that involves runes, you need to have the quest.
Mine was initially bugged in Spinward Rise; and Ive heard in other threads that theirs started in Reclaimation Rock. I'm curious if anyone has had it start anywhere that isn't an elemental evil campaign?