I had this problem in IIS 8.5 after renewing my LE certs in March 2016. The first thing I had to do was install the LE intermediate cert to the server’s Intermediate Store (as explained here). Then, despite having all the necessary intermediates installed on the server, I had to remove the old LE intermediate cert and then restart IIS. I used the tool at SSLShopper to verify that this was indeed the problem – IIS was sending the X1 intermediate instead of the X3, even though both were installed on the machine. Since my SSL cert was signed with the X3 cert, Firefox would complain that the intermediate provided (X1) did not complete the chain.
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