I have exactly the same problem as described here: IIS sends incorrect intermediate SSL certificate
Unfortunely, the answer provided by CryptoGuy does not worked for me.
I checked: I do not have the certificate in SHA1 installed on the machine (in user store, "IIS" store or machine store!!!). When I'm displaying the certificate the correct intermediate is displayed (the one in SHA256, the only one present on all store).
I have followed instructions (deleting all IIS bindings, delete certificate and private key, clear cryptoapi cache...). Also tried to reboot the server: no change! I have really no idea where IIS found this bad intermediate CA and why it's using it!