Were you able to solve this? I have the same issue.
Two popups show immediately on clicking on the glossary term. (one over the other). To dismiss, the user must dismiss both of them. It's a secondary glossary. Not global. The only glossary on a course. See pic below. (Did I double-click? No... you click once, you get two popups).
Sometimes, it's multiple popups until you dismiss one.... like one every half second, non-stop, until the first one is dismissed. Sometimes it stops after 2, or 3, or 4.... quite unpredictable.
Update: I noticed this only happens when clicking from within a course section/topic - e.g. in a label or an activity's description. If you open the activity and click on the glossary link there, it pops up correctly (once)/