Hi, I had the same issue - in our case, we created invoices from the sales orders and the sales orders still showed up under "open sales orders summary" report even though there was no remaining balance left on the sales order.  In that case, "Mark as Closed" was greyed out (as if the system already believed the sales order to be closed out).  So, I entered 

-CLOSED-

into the "Memo" field on the bottom left and it fixed the issue.  The sales orders are still in the system but they no longer show up in the open sales orders summary reports.  Give it a try, as it fixed the issue for us.  I hope this helps.