Are you setting a resolution on the closed tickets? If there is not a resolution set, I think GH will show the ticket as 'In Progress'. These scenarios are especially likely if you've created your own workflow from scratch.
Other ways to tell you have this problem (no resolution):
1) The ticket still shows up on the current assignee's Assigned to Me list
2) Issue navigator search results show status "Closed" with resolution Unresolved.
I'd check that next.
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