And another post on the IIS forum:
https://forums.iis.net/p/1230532/2117835.aspx?p=True&t=635953125359182511
I just renewed a cert using the X3 intermediate on a Linux/Apache server and it worked just fine… Guess that’s why they call the Linux web server LAMP and the Windows web server WIMP… lol
LAMP: Linux, Apache, MySQL, PHP
WIMP: Windows, IIS, Microsoft SQL, Powershell
For those of you tracking the IIS 8.5 specific issue we've discussed, there has been some activity on the Technet forum. no solution yet, but an interesting discussion around searching the local certificate stores using PowerShell in an effort to find this hidden X1 cert that keeps getting served...
https://social.technet.microsoft.com/Forums/en-US/9cd5d6c8-25e5-494d-acf2-d94230e68a9f/iis-85-on-windows-2012-r2-returns-the-incorrect-intermediate-certificate?forum=winserver8gen&prof=required
~~~~~~~~~~~~~~~~Update 4/6/2016
It seems I am limited to only 3 posts for one thread so I am posting my reply to "T917820981726". His post from 4/6/16 11:20 AM PST.
So I had this same experience on 2012 R2, however restarting the server and the IIS service didn't seem to make any difference. I am going to try again though to be sure...